From 8c36fae7f00acb023ef3c2a58ad4127fe1440c3c Mon Sep 17 00:00:00 2001 From: Suzanne Jin Date: Fri, 31 Jan 2025 14:52:48 +0000 Subject: [PATCH 01/15] [gsea] unable default seed option --- modules/nf-core/gsea/gsea/main.nf | 2 +- modules/nf-core/gsea/gsea/tests/main.nf.test | 2 ++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/modules/nf-core/gsea/gsea/main.nf b/modules/nf-core/gsea/gsea/main.nf index 494b8a5d9e4..7813308fa6f 100644 --- a/modules/nf-core/gsea/gsea/main.nf +++ b/modules/nf-core/gsea/gsea/main.nf @@ -45,7 +45,7 @@ process GSEA_GSEA { def rpt_label = prefix.replaceAll('\\.$', '') // Remove any trailing dots from prefix when passed as report label, so GSEA doesn't produce double-dotted top-level outputs def chip_command = chip ? "-chip $chip -collapse true" : '' def VERSION = '4.3.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. - if (!(args ==~ /.*-rnd_seed.*/)) {args += " -rnd_seed 10"} + // if (!(args ==~ /.*-rnd_seed.*/)) {args += " -rnd_seed 10"} // unable this for the moment, until a global seed option is set for differentialabundance pipeline """ # Run GSEA diff --git a/modules/nf-core/gsea/gsea/tests/main.nf.test b/modules/nf-core/gsea/gsea/tests/main.nf.test index 1f97e97aec0..83873d85fc7 100644 --- a/modules/nf-core/gsea/gsea/tests/main.nf.test +++ b/modules/nf-core/gsea/gsea/tests/main.nf.test @@ -12,6 +12,8 @@ nextflow_process { test("test") { + config "./nextflow.config" + when { process { """ From 425d9705d959e1a253074d7b6c9fb3e0d0d218df Mon Sep 17 00:00:00 2001 From: Suzanne Jin Date: Fri, 31 Jan 2025 14:58:20 +0000 Subject: [PATCH 02/15] [subworkflow] update abundance_differential_filter to output a list of files for variance stabilised matrices. This is to facilitate the channel handling afterwards in the differentialabundance pipeline --- .../abundance_differential_filter/main.nf | 22 +- .../abundance_differential_filter/meta.yml | 7 +- .../tests/main.nf.test.snap | 332 +++++++++--------- 3 files changed, 190 insertions(+), 171 deletions(-) diff --git a/subworkflows/nf-core/abundance_differential_filter/main.nf b/subworkflows/nf-core/abundance_differential_filter/main.nf index 8c11efa55eb..88cbbec4112 100644 --- a/subworkflows/nf-core/abundance_differential_filter/main.nf +++ b/subworkflows/nf-core/abundance_differential_filter/main.nf @@ -9,12 +9,6 @@ include { DESEQ2_DIFFERENTIAL as DESEQ2_NORM } from '../../../modules/nf-core/d include { PROPR_PROPD } from '../../../modules/nf-core/propr/propd/main' include { CUSTOM_FILTERDIFFERENTIALTABLE } from '../../../modules/nf-core/custom/filterdifferentialtable/main' -// Combine meta maps, including merging non-identical values of shared keys (e.g. 'id') -def mergeMaps(meta, meta2){ - (meta + meta2).collectEntries { k, v -> - meta[k] && meta[k] != v ? [k, "${meta[k]}_${v}"] : [k, v] - } -} workflow ABUNDANCE_DIFFERENTIAL_FILTER { take: @@ -31,7 +25,7 @@ workflow ABUNDANCE_DIFFERENTIAL_FILTER { // Set up how the channels crossed below will be used to generate channels for processing def criteria = multiMapCriteria { meta_input, abundance, analysis_method, fc_threshold, stat_threshold, meta_exp, samplesheet, meta_contrasts, variable, reference, target -> - def meta_for_diff = mergeMaps(meta_contrasts, meta_input) + [ 'method': analysis_method ] + def meta_for_diff = meta_input + meta_contrasts + [ 'method': analysis_method ] def meta_input_new = meta_input + [ 'method': analysis_method ] samples_and_matrix: [ meta_input_new, samplesheet, abundance ] @@ -131,6 +125,18 @@ workflow ABUNDANCE_DIFFERENTIAL_FILTER { ch_model = DESEQ2_DIFFERENTIAL.out.model .mix(LIMMA_DIFFERENTIAL.out.model) + ch_variance_stabilised_matrix = DESEQ2_NORM.out.rlog_counts.ifEmpty([[],[]]) + .combine(DESEQ2_NORM.out.vst_counts.ifEmpty([[],[]])) + .map { meta_rlog, rlog, meta_vst, vst -> + if (meta_rlog == meta_vst && meta_rlog != []) { + return [meta_rlog, [rlog, vst]] + } else if (meta_rlog != [] && meta_vst == []) { + return [meta_rlog, [rlog]] + } else if (meta_rlog == [] && meta_vst != []) { + return [meta_vst, [vst]] + } + } + ch_versions = DESEQ2_DIFFERENTIAL.out.versions .mix(LIMMA_DIFFERENTIAL.out.versions) .mix(PROPR_PROPD.out.versions) @@ -186,7 +192,7 @@ workflow ABUNDANCE_DIFFERENTIAL_FILTER { // other normalised_matrix = ch_normalised_matrix - variance_stabilised_matrix = DESEQ2_NORM.out.rlog_counts.mix(DESEQ2_NORM.out.vst_counts) + variance_stabilised_matrix = ch_variance_stabilised_matrix model = ch_model versions = ch_versions } diff --git a/subworkflows/nf-core/abundance_differential_filter/meta.yml b/subworkflows/nf-core/abundance_differential_filter/meta.yml index cc22f805353..8241954831e 100644 --- a/subworkflows/nf-core/abundance_differential_filter/meta.yml +++ b/subworkflows/nf-core/abundance_differential_filter/meta.yml @@ -116,10 +116,11 @@ output: - meta: type: map description: Metadata map - - matrix: - type: file - description: Variance stabilised count matrix file + - matrices: + type: list + description: A list of variance stabilised count matrix files pattern: "*.{csv,tsv}" + - model: description: Channel containing statistical model object from differential analysis structure: diff --git a/subworkflows/nf-core/abundance_differential_filter/tests/main.nf.test.snap b/subworkflows/nf-core/abundance_differential_filter/tests/main.nf.test.snap index 6795359ae88..a03d01510b7 100644 --- a/subworkflows/nf-core/abundance_differential_filter/tests/main.nf.test.snap +++ b/subworkflows/nf-core/abundance_differential_filter/tests/main.nf.test.snap @@ -4,19 +4,19 @@ [ [ { - "id": "diagnosis_normal_uremia_test", + "id": "diagnosis_normal_uremia", "variable": "diagnosis", "reference": "normal", "target": "uremia", "method": "limma" }, - "diagnosis_normal_uremia_test_limma.limma.results.tsv:md5,4f0944b54b3ab7aa6ded5dd4b4e82802" + "diagnosis_normal_uremia_limma.limma.results.tsv:md5,4f0944b54b3ab7aa6ded5dd4b4e82802" ] ], [ [ { - "id": "diagnosis_normal_uremia_test", + "id": "diagnosis_normal_uremia", "variable": "diagnosis", "reference": "normal", "target": "uremia", @@ -24,22 +24,22 @@ "fc_threshold": 1.5, "stat_threshold": 0.05 }, - "diagnosis_normal_uremia_test_filtered.tsv:md5,a971455ece4ae3c3ab902407b36fc6a5" + "diagnosis_normal_uremia_filtered.tsv:md5,a971455ece4ae3c3ab902407b36fc6a5" ] ], [ - + ], [ [ { - "id": "diagnosis_normal_uremia_test", + "id": "diagnosis_normal_uremia", "variable": "diagnosis", "reference": "normal", "target": "uremia", "method": "limma" }, - "diagnosis_normal_uremia_test_limma.limma.model.txt:md5,70b000f632b8bdba4917046362dd876b" + "diagnosis_normal_uremia_limma.limma.model.txt:md5,70b000f632b8bdba4917046362dd876b" ] ], [ @@ -48,62 +48,62 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nextflow": "24.10.4" }, - "timestamp": "2025-01-14T16:51:17.162826924" + "timestamp": "2025-01-31T13:51:00.356867156" }, "deseq2 and limma - mouse - basic": { "content": [ [ [ { - "id": "treatment_mCherry_hND6__test", + "id": "treatment_mCherry_hND6_", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "", "method": "deseq2" }, - "treatment_mCherry_hND6__test_deseq2.deseq2.results.tsv:md5,791cdba2615a445cded13cae95df73ef" + "treatment_mCherry_hND6__deseq2.deseq2.results.tsv:md5,791cdba2615a445cded13cae95df73ef" ], [ { - "id": "treatment_mCherry_hND6__test", + "id": "treatment_mCherry_hND6_", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "", "method": "limma" }, - "treatment_mCherry_hND6__test_limma_voom.limma.results.tsv:md5,ff36827b7869a8a3c3c905efedcafc93" + "treatment_mCherry_hND6__limma_voom.limma.results.tsv:md5,ff36827b7869a8a3c3c905efedcafc93" ], [ { - "id": "treatment_mCherry_hND6_sample_number_test", + "id": "treatment_mCherry_hND6_sample_number", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "sample_number", "method": "deseq2" }, - "treatment_mCherry_hND6_sample_number_test_deseq2.deseq2.results.tsv:md5,2438053a4bdc869f467a12d3c22c7ba7" + "treatment_mCherry_hND6_sample_number_deseq2.deseq2.results.tsv:md5,2438053a4bdc869f467a12d3c22c7ba7" ], [ { - "id": "treatment_mCherry_hND6_sample_number_test", + "id": "treatment_mCherry_hND6_sample_number", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "sample_number", "method": "limma" }, - "treatment_mCherry_hND6_sample_number_test_limma_voom.limma.results.tsv:md5,5f34e79dbcb5ba1908d797548921d7fc" + "treatment_mCherry_hND6_sample_number_limma_voom.limma.results.tsv:md5,5f34e79dbcb5ba1908d797548921d7fc" ] ], [ [ { - "id": "treatment_mCherry_hND6__test", + "id": "treatment_mCherry_hND6_", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -112,11 +112,11 @@ "fc_threshold": 1.5, "stat_threshold": 0.05 }, - "treatment_mCherry_hND6__test_filtered.tsv:md5,7829ead408f4c9cad4277598a231c494" + "treatment_mCherry_hND6__filtered.tsv:md5,7829ead408f4c9cad4277598a231c494" ], [ { - "id": "treatment_mCherry_hND6__test", + "id": "treatment_mCherry_hND6_", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -125,11 +125,11 @@ "fc_threshold": 1.5, "stat_threshold": 0.05 }, - "treatment_mCherry_hND6__test_filtered.tsv:md5,0bfc9215edc6aad064c3ce6abc81bfce" + "treatment_mCherry_hND6__filtered.tsv:md5,0bfc9215edc6aad064c3ce6abc81bfce" ], [ { - "id": "treatment_mCherry_hND6_sample_number_test", + "id": "treatment_mCherry_hND6_sample_number", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -138,11 +138,11 @@ "fc_threshold": 1.5, "stat_threshold": 0.05 }, - "treatment_mCherry_hND6_sample_number_test_filtered.tsv:md5,8b084475c9e7e1b34a510a73b613ff39" + "treatment_mCherry_hND6_sample_number_filtered.tsv:md5,8b084475c9e7e1b34a510a73b613ff39" ], [ { - "id": "treatment_mCherry_hND6_sample_number_test", + "id": "treatment_mCherry_hND6_sample_number", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -151,7 +151,7 @@ "fc_threshold": 1.5, "stat_threshold": 0.05 }, - "treatment_mCherry_hND6_sample_number_test_filtered.tsv:md5,0bfc9215edc6aad064c3ce6abc81bfce" + "treatment_mCherry_hND6_sample_number_filtered.tsv:md5,0bfc9215edc6aad064c3ce6abc81bfce" ] ], [ @@ -176,53 +176,55 @@ "id": "test", "method": "deseq2" }, - "test_deseq2_norm.rlog.tsv:md5,b1adc1fba6bd0c8b55973608f4b97030" + [ + "test_deseq2_norm.rlog.tsv:md5,b1adc1fba6bd0c8b55973608f4b97030" + ] ] ], [ [ { - "id": "treatment_mCherry_hND6__test", + "id": "treatment_mCherry_hND6_", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "", "method": "deseq2" }, - "treatment_mCherry_hND6__test_deseq2.deseq2.model.txt:md5,d2113d82b76046c319e6602da2ad74d6" + "treatment_mCherry_hND6__deseq2.deseq2.model.txt:md5,d2113d82b76046c319e6602da2ad74d6" ], [ { - "id": "treatment_mCherry_hND6__test", + "id": "treatment_mCherry_hND6_", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "", "method": "limma" }, - "treatment_mCherry_hND6__test_limma_voom.limma.model.txt:md5,d2113d82b76046c319e6602da2ad74d6" + "treatment_mCherry_hND6__limma_voom.limma.model.txt:md5,d2113d82b76046c319e6602da2ad74d6" ], [ { - "id": "treatment_mCherry_hND6_sample_number_test", + "id": "treatment_mCherry_hND6_sample_number", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "sample_number", "method": "deseq2" }, - "treatment_mCherry_hND6_sample_number_test_deseq2.deseq2.model.txt:md5,fa05126a58cb67c107d45426b0bdea83" + "treatment_mCherry_hND6_sample_number_deseq2.deseq2.model.txt:md5,fa05126a58cb67c107d45426b0bdea83" ], [ { - "id": "treatment_mCherry_hND6_sample_number_test", + "id": "treatment_mCherry_hND6_sample_number", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "sample_number", "method": "limma" }, - "treatment_mCherry_hND6_sample_number_test_limma_voom.limma.model.txt:md5,3b96713b4e3f027b0347859f02a9038d" + "treatment_mCherry_hND6_sample_number_limma_voom.limma.model.txt:md5,3b96713b4e3f027b0347859f02a9038d" ] ], [ @@ -234,16 +236,16 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nextflow": "24.10.4" }, - "timestamp": "2025-01-14T16:53:11.245100955" + "timestamp": "2025-01-31T13:53:24.035095649" }, "limma - voom": { "content": [ [ [ { - "id": "treatment_mCherry_hND6__test", + "id": "treatment_mCherry_hND6_", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -252,11 +254,11 @@ "fc_threshold": 1.5, "stat_threshold": 0.05 }, - "treatment_mCherry_hND6__test_filtered.tsv:md5,0bfc9215edc6aad064c3ce6abc81bfce" + "treatment_mCherry_hND6__filtered.tsv:md5,0bfc9215edc6aad064c3ce6abc81bfce" ], [ { - "id": "treatment_mCherry_hND6_sample_number_test", + "id": "treatment_mCherry_hND6_sample_number", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -265,7 +267,7 @@ "fc_threshold": 1.5, "stat_threshold": 0.05 }, - "treatment_mCherry_hND6_sample_number_test_filtered.tsv:md5,0bfc9215edc6aad064c3ce6abc81bfce" + "treatment_mCherry_hND6_sample_number_filtered.tsv:md5,0bfc9215edc6aad064c3ce6abc81bfce" ] ], [ @@ -280,25 +282,25 @@ [ [ { - "id": "treatment_mCherry_hND6__test", + "id": "treatment_mCherry_hND6_", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "", "method": "limma" }, - "treatment_mCherry_hND6__test_limma_voom.limma.model.txt:md5,d2113d82b76046c319e6602da2ad74d6" + "treatment_mCherry_hND6__limma_voom.limma.model.txt:md5,d2113d82b76046c319e6602da2ad74d6" ], [ { - "id": "treatment_mCherry_hND6_sample_number_test", + "id": "treatment_mCherry_hND6_sample_number", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "sample_number", "method": "limma" }, - "treatment_mCherry_hND6_sample_number_test_limma_voom.limma.model.txt:md5,3b96713b4e3f027b0347859f02a9038d" + "treatment_mCherry_hND6_sample_number_limma_voom.limma.model.txt:md5,3b96713b4e3f027b0347859f02a9038d" ] ], [ @@ -308,84 +310,84 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nextflow": "24.10.4" }, - "timestamp": "2025-01-14T16:51:32.460857013" + "timestamp": "2025-01-31T13:51:18.880578932" }, "deseq2 + limma-voom + propd - mouse - basic": { "content": [ [ [ { - "id": "treatment_mCherry_hND6__test", + "id": "treatment_mCherry_hND6_", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "", "method": "deseq2" }, - "treatment_mCherry_hND6__test_deseq2.deseq2.results.tsv:md5,791cdba2615a445cded13cae95df73ef" + "treatment_mCherry_hND6__deseq2.deseq2.results.tsv:md5,791cdba2615a445cded13cae95df73ef" ], [ { - "id": "treatment_mCherry_hND6__test", + "id": "treatment_mCherry_hND6_", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "", "method": "limma" }, - "treatment_mCherry_hND6__test_limma_voom.limma.results.tsv:md5,ff36827b7869a8a3c3c905efedcafc93" + "treatment_mCherry_hND6__limma_voom.limma.results.tsv:md5,ff36827b7869a8a3c3c905efedcafc93" ], [ { - "id": "treatment_mCherry_hND6__test", + "id": "treatment_mCherry_hND6_", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "", "method": "propd" }, - "treatment_mCherry_hND6__test_propd.propd.genewise.tsv:md5,bdc19a4b7430f248cd332287b630c872" + "treatment_mCherry_hND6__propd.propd.genewise.tsv:md5,bdc19a4b7430f248cd332287b630c872" ], [ { - "id": "treatment_mCherry_hND6_sample_number_test", + "id": "treatment_mCherry_hND6_sample_number", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "sample_number", "method": "deseq2" }, - "treatment_mCherry_hND6_sample_number_test_deseq2.deseq2.results.tsv:md5,2438053a4bdc869f467a12d3c22c7ba7" + "treatment_mCherry_hND6_sample_number_deseq2.deseq2.results.tsv:md5,2438053a4bdc869f467a12d3c22c7ba7" ], [ { - "id": "treatment_mCherry_hND6_sample_number_test", + "id": "treatment_mCherry_hND6_sample_number", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "sample_number", "method": "limma" }, - "treatment_mCherry_hND6_sample_number_test_limma_voom.limma.results.tsv:md5,5f34e79dbcb5ba1908d797548921d7fc" + "treatment_mCherry_hND6_sample_number_limma_voom.limma.results.tsv:md5,5f34e79dbcb5ba1908d797548921d7fc" ], [ { - "id": "treatment_mCherry_hND6_sample_number_test", + "id": "treatment_mCherry_hND6_sample_number", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "sample_number", "method": "propd" }, - "treatment_mCherry_hND6_sample_number_test_propd.propd.genewise.tsv:md5,bdc19a4b7430f248cd332287b630c872" + "treatment_mCherry_hND6_sample_number_propd.propd.genewise.tsv:md5,bdc19a4b7430f248cd332287b630c872" ] ], [ [ { - "id": "treatment_mCherry_hND6__test", + "id": "treatment_mCherry_hND6_", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -394,11 +396,11 @@ "fc_threshold": 1.5, "stat_threshold": 0.05 }, - "treatment_mCherry_hND6__test_filtered.tsv:md5,7829ead408f4c9cad4277598a231c494" + "treatment_mCherry_hND6__filtered.tsv:md5,7829ead408f4c9cad4277598a231c494" ], [ { - "id": "treatment_mCherry_hND6__test", + "id": "treatment_mCherry_hND6_", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -407,11 +409,11 @@ "fc_threshold": 1.5, "stat_threshold": 0.05 }, - "treatment_mCherry_hND6__test_filtered.tsv:md5,0bfc9215edc6aad064c3ce6abc81bfce" + "treatment_mCherry_hND6__filtered.tsv:md5,0bfc9215edc6aad064c3ce6abc81bfce" ], [ { - "id": "treatment_mCherry_hND6__test", + "id": "treatment_mCherry_hND6_", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -420,11 +422,11 @@ "fc_threshold": 1.5, "stat_threshold": 100 }, - "treatment_mCherry_hND6__test_filtered.tsv:md5,432b2ba4e63fd8f7e2aee74e5b71b0a5" + "treatment_mCherry_hND6__filtered.tsv:md5,432b2ba4e63fd8f7e2aee74e5b71b0a5" ], [ { - "id": "treatment_mCherry_hND6_sample_number_test", + "id": "treatment_mCherry_hND6_sample_number", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -433,11 +435,11 @@ "fc_threshold": 1.5, "stat_threshold": 0.05 }, - "treatment_mCherry_hND6_sample_number_test_filtered.tsv:md5,8b084475c9e7e1b34a510a73b613ff39" + "treatment_mCherry_hND6_sample_number_filtered.tsv:md5,8b084475c9e7e1b34a510a73b613ff39" ], [ { - "id": "treatment_mCherry_hND6_sample_number_test", + "id": "treatment_mCherry_hND6_sample_number", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -446,11 +448,11 @@ "fc_threshold": 1.5, "stat_threshold": 0.05 }, - "treatment_mCherry_hND6_sample_number_test_filtered.tsv:md5,0bfc9215edc6aad064c3ce6abc81bfce" + "treatment_mCherry_hND6_sample_number_filtered.tsv:md5,0bfc9215edc6aad064c3ce6abc81bfce" ], [ { - "id": "treatment_mCherry_hND6_sample_number_test", + "id": "treatment_mCherry_hND6_sample_number", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -459,31 +461,31 @@ "fc_threshold": 1.5, "stat_threshold": 100 }, - "treatment_mCherry_hND6_sample_number_test_filtered.tsv:md5,432b2ba4e63fd8f7e2aee74e5b71b0a5" + "treatment_mCherry_hND6_sample_number_filtered.tsv:md5,432b2ba4e63fd8f7e2aee74e5b71b0a5" ] ], [ [ { - "id": "treatment_mCherry_hND6__test", + "id": "treatment_mCherry_hND6_", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "", "method": "propd" }, - "treatment_mCherry_hND6__test_propd.propd.adjacency.csv:md5,3a947ffd8172990c6207aa7561a41cb8" + "treatment_mCherry_hND6__propd.propd.adjacency.csv:md5,3a947ffd8172990c6207aa7561a41cb8" ], [ { - "id": "treatment_mCherry_hND6_sample_number_test", + "id": "treatment_mCherry_hND6_sample_number", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "sample_number", "method": "propd" }, - "treatment_mCherry_hND6_sample_number_test_propd.propd.adjacency.csv:md5,3a947ffd8172990c6207aa7561a41cb8" + "treatment_mCherry_hND6_sample_number_propd.propd.adjacency.csv:md5,3a947ffd8172990c6207aa7561a41cb8" ] ], [ @@ -508,53 +510,55 @@ "id": "test", "method": "deseq2" }, - "test_deseq2_norm.rlog.tsv:md5,b1adc1fba6bd0c8b55973608f4b97030" + [ + "test_deseq2_norm.rlog.tsv:md5,b1adc1fba6bd0c8b55973608f4b97030" + ] ] ], [ [ { - "id": "treatment_mCherry_hND6__test", + "id": "treatment_mCherry_hND6_", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "", "method": "deseq2" }, - "treatment_mCherry_hND6__test_deseq2.deseq2.model.txt:md5,d2113d82b76046c319e6602da2ad74d6" + "treatment_mCherry_hND6__deseq2.deseq2.model.txt:md5,d2113d82b76046c319e6602da2ad74d6" ], [ { - "id": "treatment_mCherry_hND6__test", + "id": "treatment_mCherry_hND6_", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "", "method": "limma" }, - "treatment_mCherry_hND6__test_limma_voom.limma.model.txt:md5,d2113d82b76046c319e6602da2ad74d6" + "treatment_mCherry_hND6__limma_voom.limma.model.txt:md5,d2113d82b76046c319e6602da2ad74d6" ], [ { - "id": "treatment_mCherry_hND6_sample_number_test", + "id": "treatment_mCherry_hND6_sample_number", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "sample_number", "method": "deseq2" }, - "treatment_mCherry_hND6_sample_number_test_deseq2.deseq2.model.txt:md5,fa05126a58cb67c107d45426b0bdea83" + "treatment_mCherry_hND6_sample_number_deseq2.deseq2.model.txt:md5,fa05126a58cb67c107d45426b0bdea83" ], [ { - "id": "treatment_mCherry_hND6_sample_number_test", + "id": "treatment_mCherry_hND6_sample_number", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "sample_number", "method": "limma" }, - "treatment_mCherry_hND6_sample_number_test_limma_voom.limma.model.txt:md5,3b96713b4e3f027b0347859f02a9038d" + "treatment_mCherry_hND6_sample_number_limma_voom.limma.model.txt:md5,3b96713b4e3f027b0347859f02a9038d" ] ], [ @@ -568,9 +572,9 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nextflow": "24.10.4" }, - "timestamp": "2025-01-14T16:53:54.80697542" + "timestamp": "2025-01-31T13:54:15.858310302" }, "stub": { "content": [ @@ -578,31 +582,31 @@ "0": [ [ { - "id": "treatment_mCherry_hND6__test", + "id": "treatment_mCherry_hND6_", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "", "method": "deseq2" }, - "treatment_mCherry_hND6__test.deseq2.results.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + "treatment_mCherry_hND6_.deseq2.results.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ], [ { - "id": "treatment_mCherry_hND6_sample_number_test", + "id": "treatment_mCherry_hND6_sample_number", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "sample_number", "method": "deseq2" }, - "treatment_mCherry_hND6_sample_number_test.deseq2.results.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + "treatment_mCherry_hND6_sample_number.deseq2.results.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "1": [ [ { - "id": "treatment_mCherry_hND6__test", + "id": "treatment_mCherry_hND6_", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -611,11 +615,11 @@ "fc_threshold": 1.5, "stat_threshold": 0.05 }, - "treatment_mCherry_hND6__test_filtered.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + "treatment_mCherry_hND6__filtered.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ], [ { - "id": "treatment_mCherry_hND6_sample_number_test", + "id": "treatment_mCherry_hND6_sample_number", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -624,11 +628,11 @@ "fc_threshold": 1.5, "stat_threshold": 0.05 }, - "treatment_mCherry_hND6_sample_number_test_filtered.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + "treatment_mCherry_hND6_sample_number_filtered.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "2": [ - + ], "3": [ [ @@ -645,31 +649,33 @@ "id": "test", "method": "deseq2" }, - "test.rlog.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + [ + "test.rlog.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ] ], "5": [ [ { - "id": "treatment_mCherry_hND6__test", + "id": "treatment_mCherry_hND6_", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "", "method": "deseq2" }, - "treatment_mCherry_hND6__test.deseq2.model.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + "treatment_mCherry_hND6_.deseq2.model.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ], [ { - "id": "treatment_mCherry_hND6_sample_number_test", + "id": "treatment_mCherry_hND6_sample_number", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "sample_number", "method": "deseq2" }, - "treatment_mCherry_hND6_sample_number_test.deseq2.model.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + "treatment_mCherry_hND6_sample_number.deseq2.model.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "6": [ @@ -677,30 +683,30 @@ "versions.yml:md5,05e3901f6d78f8839a7e07f422e9bc03" ], "adjacency": [ - + ], "model": [ [ { - "id": "treatment_mCherry_hND6__test", + "id": "treatment_mCherry_hND6_", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "", "method": "deseq2" }, - "treatment_mCherry_hND6__test.deseq2.model.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + "treatment_mCherry_hND6_.deseq2.model.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ], [ { - "id": "treatment_mCherry_hND6_sample_number_test", + "id": "treatment_mCherry_hND6_sample_number", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "sample_number", "method": "deseq2" }, - "treatment_mCherry_hND6_sample_number_test.deseq2.model.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + "treatment_mCherry_hND6_sample_number.deseq2.model.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "normalised_matrix": [ @@ -715,31 +721,31 @@ "results_genewise": [ [ { - "id": "treatment_mCherry_hND6__test", + "id": "treatment_mCherry_hND6_", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "", "method": "deseq2" }, - "treatment_mCherry_hND6__test.deseq2.results.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + "treatment_mCherry_hND6_.deseq2.results.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ], [ { - "id": "treatment_mCherry_hND6_sample_number_test", + "id": "treatment_mCherry_hND6_sample_number", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "sample_number", "method": "deseq2" }, - "treatment_mCherry_hND6_sample_number_test.deseq2.results.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + "treatment_mCherry_hND6_sample_number.deseq2.results.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "results_genewise_filtered": [ [ { - "id": "treatment_mCherry_hND6__test", + "id": "treatment_mCherry_hND6_", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -748,11 +754,11 @@ "fc_threshold": 1.5, "stat_threshold": 0.05 }, - "treatment_mCherry_hND6__test_filtered.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + "treatment_mCherry_hND6__filtered.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ], [ { - "id": "treatment_mCherry_hND6_sample_number_test", + "id": "treatment_mCherry_hND6_sample_number", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -761,7 +767,7 @@ "fc_threshold": 1.5, "stat_threshold": 0.05 }, - "treatment_mCherry_hND6_sample_number_test_filtered.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + "treatment_mCherry_hND6_sample_number_filtered.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "variance_stabilised_matrix": [ @@ -770,7 +776,9 @@ "id": "test", "method": "deseq2" }, - "test.rlog.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + [ + "test.rlog.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ] ], "versions": [ @@ -781,40 +789,40 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nextflow": "24.10.4" }, - "timestamp": "2025-01-14T16:54:12.823125892" + "timestamp": "2025-01-31T13:54:38.936440968" }, "deseq2 - mouse - basic": { "content": [ [ [ { - "id": "treatment_mCherry_hND6__test", + "id": "treatment_mCherry_hND6_", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "", "method": "deseq2" }, - "treatment_mCherry_hND6__test_deseq2.deseq2.results.tsv:md5,791cdba2615a445cded13cae95df73ef" + "treatment_mCherry_hND6__deseq2.deseq2.results.tsv:md5,791cdba2615a445cded13cae95df73ef" ], [ { - "id": "treatment_mCherry_hND6_sample_number_test", + "id": "treatment_mCherry_hND6_sample_number", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "sample_number", "method": "deseq2" }, - "treatment_mCherry_hND6_sample_number_test_deseq2.deseq2.results.tsv:md5,2438053a4bdc869f467a12d3c22c7ba7" + "treatment_mCherry_hND6_sample_number_deseq2.deseq2.results.tsv:md5,2438053a4bdc869f467a12d3c22c7ba7" ] ], [ [ { - "id": "treatment_mCherry_hND6__test", + "id": "treatment_mCherry_hND6_", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -823,11 +831,11 @@ "fc_threshold": 1.5, "stat_threshold": 0.05 }, - "treatment_mCherry_hND6__test_filtered.tsv:md5,7829ead408f4c9cad4277598a231c494" + "treatment_mCherry_hND6__filtered.tsv:md5,7829ead408f4c9cad4277598a231c494" ], [ { - "id": "treatment_mCherry_hND6_sample_number_test", + "id": "treatment_mCherry_hND6_sample_number", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -836,7 +844,7 @@ "fc_threshold": 1.5, "stat_threshold": 0.05 }, - "treatment_mCherry_hND6_sample_number_test_filtered.tsv:md5,8b084475c9e7e1b34a510a73b613ff39" + "treatment_mCherry_hND6_sample_number_filtered.tsv:md5,8b084475c9e7e1b34a510a73b613ff39" ] ], [ @@ -854,31 +862,33 @@ "id": "test", "method": "deseq2" }, - "test_deseq2_norm.rlog.tsv:md5,b1adc1fba6bd0c8b55973608f4b97030" + [ + "test_deseq2_norm.rlog.tsv:md5,b1adc1fba6bd0c8b55973608f4b97030" + ] ] ], [ [ { - "id": "treatment_mCherry_hND6__test", + "id": "treatment_mCherry_hND6_", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "", "method": "deseq2" }, - "treatment_mCherry_hND6__test_deseq2.deseq2.model.txt:md5,d2113d82b76046c319e6602da2ad74d6" + "treatment_mCherry_hND6__deseq2.deseq2.model.txt:md5,d2113d82b76046c319e6602da2ad74d6" ], [ { - "id": "treatment_mCherry_hND6_sample_number_test", + "id": "treatment_mCherry_hND6_sample_number", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "sample_number", "method": "deseq2" }, - "treatment_mCherry_hND6_sample_number_test_deseq2.deseq2.model.txt:md5,fa05126a58cb67c107d45426b0bdea83" + "treatment_mCherry_hND6_sample_number_deseq2.deseq2.model.txt:md5,fa05126a58cb67c107d45426b0bdea83" ] ], [ @@ -888,40 +898,40 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nextflow": "24.10.4" }, - "timestamp": "2025-01-14T16:50:35.085607799" + "timestamp": "2025-01-31T13:49:54.987152774" }, "deseq2 - with transcript lengths": { "content": [ [ [ { - "id": "treatment_mCherry_hND6__test", + "id": "treatment_mCherry_hND6_", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "", "method": "deseq2" }, - "treatment_mCherry_hND6__test_deseq2.deseq2.results.tsv:md5,944176b73455aa7c8de3ec32c03edef6" + "treatment_mCherry_hND6__deseq2.deseq2.results.tsv:md5,944176b73455aa7c8de3ec32c03edef6" ], [ { - "id": "treatment_mCherry_hND6_sample_number_test", + "id": "treatment_mCherry_hND6_sample_number", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "sample_number", "method": "deseq2" }, - "treatment_mCherry_hND6_sample_number_test_deseq2.deseq2.results.tsv:md5,6a9bc76c9d54034c90fa159372f97516" + "treatment_mCherry_hND6_sample_number_deseq2.deseq2.results.tsv:md5,6a9bc76c9d54034c90fa159372f97516" ] ], [ [ { - "id": "treatment_mCherry_hND6__test", + "id": "treatment_mCherry_hND6_", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -930,11 +940,11 @@ "fc_threshold": 1.5, "stat_threshold": 0.05 }, - "treatment_mCherry_hND6__test_filtered.tsv:md5,a48241fb5f24d961d3cce208f060b624" + "treatment_mCherry_hND6__filtered.tsv:md5,a48241fb5f24d961d3cce208f060b624" ], [ { - "id": "treatment_mCherry_hND6_sample_number_test", + "id": "treatment_mCherry_hND6_sample_number", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -943,7 +953,7 @@ "fc_threshold": 1.5, "stat_threshold": 0.05 }, - "treatment_mCherry_hND6_sample_number_test_filtered.tsv:md5,04d6911dce789f284c929694aa3d99b0" + "treatment_mCherry_hND6_sample_number_filtered.tsv:md5,04d6911dce789f284c929694aa3d99b0" ] ], [ @@ -961,31 +971,33 @@ "id": "test", "method": "deseq2" }, - "test_deseq2_norm.rlog.tsv:md5,22a4b117246b2317e0f4daf7919703f2" + [ + "test_deseq2_norm.rlog.tsv:md5,22a4b117246b2317e0f4daf7919703f2" + ] ] ], [ [ { - "id": "treatment_mCherry_hND6__test", + "id": "treatment_mCherry_hND6_", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "", "method": "deseq2" }, - "treatment_mCherry_hND6__test_deseq2.deseq2.model.txt:md5,d2113d82b76046c319e6602da2ad74d6" + "treatment_mCherry_hND6__deseq2.deseq2.model.txt:md5,d2113d82b76046c319e6602da2ad74d6" ], [ { - "id": "treatment_mCherry_hND6_sample_number_test", + "id": "treatment_mCherry_hND6_sample_number", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "sample_number", "method": "deseq2" }, - "treatment_mCherry_hND6_sample_number_test_deseq2.deseq2.model.txt:md5,fa05126a58cb67c107d45426b0bdea83" + "treatment_mCherry_hND6_sample_number_deseq2.deseq2.model.txt:md5,fa05126a58cb67c107d45426b0bdea83" ] ], [ @@ -995,40 +1007,40 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nextflow": "24.10.4" }, - "timestamp": "2025-01-14T16:52:07.822745077" + "timestamp": "2025-01-31T13:52:00.181604697" }, "propd - mouse - basic": { "content": [ [ [ { - "id": "treatment_mCherry_hND6__test", + "id": "treatment_mCherry_hND6_", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "", "method": "propd" }, - "treatment_mCherry_hND6__test.propd.genewise.tsv:md5,bdc19a4b7430f248cd332287b630c872" + "treatment_mCherry_hND6_.propd.genewise.tsv:md5,bdc19a4b7430f248cd332287b630c872" ], [ { - "id": "treatment_mCherry_hND6_sample_number_test", + "id": "treatment_mCherry_hND6_sample_number", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "sample_number", "method": "propd" }, - "treatment_mCherry_hND6_sample_number_test.propd.genewise.tsv:md5,bdc19a4b7430f248cd332287b630c872" + "treatment_mCherry_hND6_sample_number.propd.genewise.tsv:md5,bdc19a4b7430f248cd332287b630c872" ] ], [ [ { - "id": "treatment_mCherry_hND6__test", + "id": "treatment_mCherry_hND6_", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -1037,11 +1049,11 @@ "fc_threshold": 1.5, "stat_threshold": 100 }, - "treatment_mCherry_hND6__test_filtered.tsv:md5,432b2ba4e63fd8f7e2aee74e5b71b0a5" + "treatment_mCherry_hND6__filtered.tsv:md5,432b2ba4e63fd8f7e2aee74e5b71b0a5" ], [ { - "id": "treatment_mCherry_hND6_sample_number_test", + "id": "treatment_mCherry_hND6_sample_number", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -1050,31 +1062,31 @@ "fc_threshold": 1.5, "stat_threshold": 100 }, - "treatment_mCherry_hND6_sample_number_test_filtered.tsv:md5,432b2ba4e63fd8f7e2aee74e5b71b0a5" + "treatment_mCherry_hND6_sample_number_filtered.tsv:md5,432b2ba4e63fd8f7e2aee74e5b71b0a5" ] ], [ [ { - "id": "treatment_mCherry_hND6__test", + "id": "treatment_mCherry_hND6_", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "", "method": "propd" }, - "treatment_mCherry_hND6__test.propd.adjacency.csv:md5,3a947ffd8172990c6207aa7561a41cb8" + "treatment_mCherry_hND6_.propd.adjacency.csv:md5,3a947ffd8172990c6207aa7561a41cb8" ], [ { - "id": "treatment_mCherry_hND6_sample_number_test", + "id": "treatment_mCherry_hND6_sample_number", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "sample_number", "method": "propd" }, - "treatment_mCherry_hND6_sample_number_test.propd.adjacency.csv:md5,3a947ffd8172990c6207aa7561a41cb8" + "treatment_mCherry_hND6_sample_number.propd.adjacency.csv:md5,3a947ffd8172990c6207aa7561a41cb8" ] ], [ @@ -1084,8 +1096,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nextflow": "24.10.4" }, - "timestamp": "2025-01-14T16:52:25.336720308" + "timestamp": "2025-01-31T13:52:39.024496481" } -} \ No newline at end of file +} From 2841259a77f0c23f8da1e184d4c117bd8db3b576 Mon Sep 17 00:00:00 2001 From: Suzanne Jin Date: Fri, 31 Jan 2025 14:59:21 +0000 Subject: [PATCH 03/15] [gsea] add module test config --- modules/nf-core/gsea/gsea/tests/nextflow.config | 5 +++++ 1 file changed, 5 insertions(+) create mode 100644 modules/nf-core/gsea/gsea/tests/nextflow.config diff --git a/modules/nf-core/gsea/gsea/tests/nextflow.config b/modules/nf-core/gsea/gsea/tests/nextflow.config new file mode 100644 index 00000000000..ff65b562a0e --- /dev/null +++ b/modules/nf-core/gsea/gsea/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: 'GSEA_GSEA' { + ext.args = { "-rnd_seed 10" } + } +} From 0aad0e95ba6e20856059dc7fd12c64b1810aea23 Mon Sep 17 00:00:00 2001 From: Suzanne Jin Date: Fri, 31 Jan 2025 15:28:14 +0000 Subject: [PATCH 04/15] update functional subworkflow. Also update gprofiler2 related snapshots - as they changed after database update --- .../gprofiler2/gost/tests/main.nf.test.snap | 28 ++- .../main.nf | 8 +- .../tests/main.nf.test.snap | 199 +++++++++--------- 3 files changed, 112 insertions(+), 123 deletions(-) diff --git a/modules/nf-core/gprofiler2/gost/tests/main.nf.test.snap b/modules/nf-core/gprofiler2/gost/tests/main.nf.test.snap index eec8d87cc62..189aee66a03 100644 --- a/modules/nf-core/gprofiler2/gost/tests/main.nf.test.snap +++ b/modules/nf-core/gprofiler2/gost/tests/main.nf.test.snap @@ -10,7 +10,7 @@ "target": "KO", "blocking": "batch" }, - "Condition_genotype_WT_KO.gprofiler2.all_enriched_pathways.tsv:md5,1134a02ca061c463bcbff277eefbfb19" + "Condition_genotype_WT_KO.gprofiler2.all_enriched_pathways.tsv:md5,396712577c32213078d1604b1ba247de" ] ], [ @@ -23,15 +23,14 @@ "blocking": "batch" }, [ - "Condition_genotype_WT_KO.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,d527b94cdb160070bcaa0bfb0cecf914", - "Condition_genotype_WT_KO.gprofiler2.GO:CC.sub_enriched_pathways.tsv:md5,ef418c3f06d50446317928e37ec8ddfb", - "Condition_genotype_WT_KO.gprofiler2.GO:MF.sub_enriched_pathways.tsv:md5,e460d4917feb0b64d334a528f59e0731", - "Condition_genotype_WT_KO.gprofiler2.HP.sub_enriched_pathways.tsv:md5,865d8f092503552831c51d775a98c6eb", - "Condition_genotype_WT_KO.gprofiler2.KEGG.sub_enriched_pathways.tsv:md5,413724002abe683f376ea914d4f21ade", - "Condition_genotype_WT_KO.gprofiler2.MIRNA.sub_enriched_pathways.tsv:md5,fce81051d7af955ddb2925ba2da9ff57", - "Condition_genotype_WT_KO.gprofiler2.REAC.sub_enriched_pathways.tsv:md5,e89e1876698ea644671a0720c85f4dbb", - "Condition_genotype_WT_KO.gprofiler2.TF.sub_enriched_pathways.tsv:md5,e272217ec7fcf01ea463ab8bcc8335cf", - "Condition_genotype_WT_KO.gprofiler2.WP.sub_enriched_pathways.tsv:md5,fdd1efa836d85bb127e933e925290cba" + "Condition_genotype_WT_KO.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,d6bebdcb2401a7f7de0ec42ad2f4521d", + "Condition_genotype_WT_KO.gprofiler2.GO:CC.sub_enriched_pathways.tsv:md5,98a49b69f8b724d88d6367dea494ca53", + "Condition_genotype_WT_KO.gprofiler2.GO:MF.sub_enriched_pathways.tsv:md5,39ce8238319df47708df78b1c461a89d", + "Condition_genotype_WT_KO.gprofiler2.HP.sub_enriched_pathways.tsv:md5,616f3a5d19844001bb8aac38049e987a", + "Condition_genotype_WT_KO.gprofiler2.MIRNA.sub_enriched_pathways.tsv:md5,486ed1510dc8bba867686b021d6e6339", + "Condition_genotype_WT_KO.gprofiler2.REAC.sub_enriched_pathways.tsv:md5,3571ac765c47e1c38c63c463465f2a1e", + "Condition_genotype_WT_KO.gprofiler2.TF.sub_enriched_pathways.tsv:md5,032491e63bb381cc9a4d7740473efc5b", + "Condition_genotype_WT_KO.gprofiler2.WP.sub_enriched_pathways.tsv:md5,e99c42df912a9ee75c7197f92d615979" ] ] ], @@ -41,14 +40,13 @@ "Condition_genotype_WT_KO.gprofiler2.GO:CC.sub_enriched_pathways.png", "Condition_genotype_WT_KO.gprofiler2.GO:MF.sub_enriched_pathways.png", "Condition_genotype_WT_KO.gprofiler2.HP.sub_enriched_pathways.png", - "Condition_genotype_WT_KO.gprofiler2.KEGG.sub_enriched_pathways.png", "Condition_genotype_WT_KO.gprofiler2.MIRNA.sub_enriched_pathways.png", "Condition_genotype_WT_KO.gprofiler2.REAC.sub_enriched_pathways.png", "Condition_genotype_WT_KO.gprofiler2.TF.sub_enriched_pathways.png", "Condition_genotype_WT_KO.gprofiler2.WP.sub_enriched_pathways.png" ], [ - + ], [ "R_sessionInfo.log" @@ -65,9 +63,9 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nextflow": "24.10.4" }, - "timestamp": "2025-01-21T11:29:54.746689985" + "timestamp": "2025-01-31T15:16:54.617930264" }, "stub": { "content": [ @@ -278,4 +276,4 @@ }, "timestamp": "2025-01-21T11:31:33.394855046" } -} \ No newline at end of file +} diff --git a/subworkflows/nf-core/differential_functional_enrichment/main.nf b/subworkflows/nf-core/differential_functional_enrichment/main.nf index ff18aedc0f6..a2e3d0cc5ba 100644 --- a/subworkflows/nf-core/differential_functional_enrichment/main.nf +++ b/subworkflows/nf-core/differential_functional_enrichment/main.nf @@ -9,12 +9,6 @@ include { CUSTOM_TABULARTOGSEACHIP } from '../../../modules/nf-core/custom/tabul include { GSEA_GSEA } from '../../../modules/nf-core/gsea/gsea/main.nf' include { PROPR_GREA } from "../../../modules/nf-core/propr/grea/main.nf" -// Combine meta maps, including merging non-identical values of shared keys (e.g. 'id') -def mergeMaps(meta, meta2){ - (meta + meta2).collectEntries { k, v -> - meta[k] && meta[k] != v ? [k, "${meta[k]}_${v}"] : [k, v] - } -} workflow DIFFERENTIAL_FUNCTIONAL_ENRICHMENT { take: @@ -55,7 +49,7 @@ workflow DIFFERENTIAL_FUNCTIONAL_ENRICHMENT { def criteria = multiMapCriteria { meta_input, input, genesets, meta_exp, samplesheet, featuresheet, features_id, features_symbol, meta_contrasts, variable, reference, target -> def meta_contrasts_new = meta_contrasts + [ 'variable': variable, 'reference': reference, 'target': target ] // make sure variable, reference, target are in the meta - def meta_all = mergeMaps(meta_contrasts_new, meta_input) + def meta_all = meta_input + meta_contrasts_new input: [ meta_all, input ] genesets: diff --git a/subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test.snap b/subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test.snap index 5591114c959..9fd49d0fa47 100644 --- a/subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test.snap +++ b/subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test.snap @@ -4,7 +4,7 @@ [ [ { - "id": "treatment_mCherry_hND6__test", + "id": "treatment_mCherry_hND6_", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -14,11 +14,11 @@ "method_de": "deseq2", "method": "gprofiler2" }, - "treatment_mCherry_hND6__test.gprofiler2.all_enriched_pathways.tsv:md5,d586d92fb6cc3e41d493d14c4d9a7d92" + "treatment_mCherry_hND6_.gprofiler2.all_enriched_pathways.tsv:md5,10f7cef4ef0e1b0eab79818fdbaab9ad" ], [ { - "id": "treatment_mCherry_hND6__test", + "id": "treatment_mCherry_hND6_", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -28,11 +28,11 @@ "method_de": "limma", "method": "gprofiler2" }, - "treatment_mCherry_hND6__test.gprofiler2.all_enriched_pathways.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + "treatment_mCherry_hND6_.gprofiler2.all_enriched_pathways.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ], [ { - "id": "treatment_mCherry_hND6__test", + "id": "treatment_mCherry_hND6_", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -42,11 +42,11 @@ "method_de": "propd", "method": "gprofiler2" }, - "treatment_mCherry_hND6__test.gprofiler2.all_enriched_pathways.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + "treatment_mCherry_hND6_.gprofiler2.all_enriched_pathways.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ], [ { - "id": "treatment_mCherry_hND6_sample_number_test", + "id": "treatment_mCherry_hND6_sample_number", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -56,11 +56,11 @@ "method_de": "deseq2", "method": "gprofiler2" }, - "treatment_mCherry_hND6_sample_number_test.gprofiler2.all_enriched_pathways.tsv:md5,fa880c70d06f56d8dad0ac8078e6233c" + "treatment_mCherry_hND6_sample_number.gprofiler2.all_enriched_pathways.tsv:md5,7ac2c2f5c0ad3d72769419f065cb6ace" ], [ { - "id": "treatment_mCherry_hND6_sample_number_test", + "id": "treatment_mCherry_hND6_sample_number", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -70,11 +70,11 @@ "method_de": "limma", "method": "gprofiler2" }, - "treatment_mCherry_hND6_sample_number_test.gprofiler2.all_enriched_pathways.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + "treatment_mCherry_hND6_sample_number.gprofiler2.all_enriched_pathways.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ], [ { - "id": "treatment_mCherry_hND6_sample_number_test", + "id": "treatment_mCherry_hND6_sample_number", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -84,13 +84,13 @@ "method_de": "propd", "method": "gprofiler2" }, - "treatment_mCherry_hND6_sample_number_test.gprofiler2.all_enriched_pathways.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + "treatment_mCherry_hND6_sample_number.gprofiler2.all_enriched_pathways.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], [ [ { - "id": "treatment_mCherry_hND6__test", + "id": "treatment_mCherry_hND6_", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -101,15 +101,15 @@ "method": "gprofiler2" }, [ - "treatment_mCherry_hND6__test.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,4c95059438af872253aa95a5ff127fca", - "treatment_mCherry_hND6__test.gprofiler2.GO:CC.sub_enriched_pathways.tsv:md5,b4e4009e067f723694efc1a46a609e2b", - "treatment_mCherry_hND6__test.gprofiler2.GO:MF.sub_enriched_pathways.tsv:md5,ece72606ce6d1d037cfd5f5b198233a8", - "treatment_mCherry_hND6__test.gprofiler2.REAC.sub_enriched_pathways.tsv:md5,dc7b6f67903e25076ab95a7e1bb39bbe" + "treatment_mCherry_hND6_.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,6047ffd74fe8a49db9b924485a441948", + "treatment_mCherry_hND6_.gprofiler2.GO:CC.sub_enriched_pathways.tsv:md5,891018299a66d62fbe979a56e9f31035", + "treatment_mCherry_hND6_.gprofiler2.GO:MF.sub_enriched_pathways.tsv:md5,46bb279062af777060495d56ac9767d7", + "treatment_mCherry_hND6_.gprofiler2.REAC.sub_enriched_pathways.tsv:md5,ca5e92673eb17242477e9c2787d68323" ] ], [ { - "id": "treatment_mCherry_hND6_sample_number_test", + "id": "treatment_mCherry_hND6_sample_number", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -120,76 +120,75 @@ "method": "gprofiler2" }, [ - "treatment_mCherry_hND6_sample_number_test.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,dc27af1c941636f8b03e8c8724773725", - "treatment_mCherry_hND6_sample_number_test.gprofiler2.GO:CC.sub_enriched_pathways.tsv:md5,09b7770d59d2efa8a58f300a16a41ae7", - "treatment_mCherry_hND6_sample_number_test.gprofiler2.GO:MF.sub_enriched_pathways.tsv:md5,a261d658ca1b1ec0511e55da734d7810", - "treatment_mCherry_hND6_sample_number_test.gprofiler2.KEGG.sub_enriched_pathways.tsv:md5,3cbdbbb1c5b232ab73d35d4a0953d19c", - "treatment_mCherry_hND6_sample_number_test.gprofiler2.REAC.sub_enriched_pathways.tsv:md5,8472cb5792bf7ec044bb95df356ad47e" + "treatment_mCherry_hND6_sample_number.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,f55e010f72ee9200624137f42e94a5e5", + "treatment_mCherry_hND6_sample_number.gprofiler2.GO:CC.sub_enriched_pathways.tsv:md5,5bb51d9184e7257ce6cdd0ce7db16923", + "treatment_mCherry_hND6_sample_number.gprofiler2.GO:MF.sub_enriched_pathways.tsv:md5,210e4b99919354c79b37e12c83fdeaa5", + "treatment_mCherry_hND6_sample_number.gprofiler2.REAC.sub_enriched_pathways.tsv:md5,d754c55c2a2a1b8acda1c663165b4d2b" ] ] ], [ - "treatment_mCherry_hND6__test.gprofiler2.gostplot.html", - "treatment_mCherry_hND6_sample_number_test.gprofiler2.gostplot.html" + "treatment_mCherry_hND6_.gprofiler2.gostplot.html", + "treatment_mCherry_hND6_sample_number.gprofiler2.gostplot.html" ], [ [ { - "id": "treatment_mCherry_hND6__test", + "id": "treatment_mCherry_hND6_", + "method_de": "deseq2", + "method": "gsea", "variable": "treatment", "reference": "mCherry", "target": "hND6", - "blocking": "", - "method_de": "deseq2", - "method": "gsea" + "blocking": "" }, - "treatment_mCherry_hND6__test.mh.all.v2022.1.Mm.symbols.gsea_report_for_mCherry.tsv:md5,ce8792382ae299749445767ff16aaecc", - "treatment_mCherry_hND6__test.mh.all.v2022.1.Mm.symbols.gsea_report_for_hND6.tsv:md5,354a961c7e1417db2bf1f7e8d00c54f0" + "treatment_mCherry_hND6_.mh.all.v2022.1.Mm.symbols.gsea_report_for_mCherry.tsv:md5,ce8792382ae299749445767ff16aaecc", + "treatment_mCherry_hND6_.mh.all.v2022.1.Mm.symbols.gsea_report_for_hND6.tsv:md5,354a961c7e1417db2bf1f7e8d00c54f0" ], [ { - "id": "treatment_mCherry_hND6__test", + "id": "treatment_mCherry_hND6_", + "method_de": "limma", + "method": "gsea", "variable": "treatment", "reference": "mCherry", "target": "hND6", - "blocking": "", - "method_de": "limma", - "method": "gsea" + "blocking": "" }, - "treatment_mCherry_hND6__test.mh.all.v2022.1.Mm.symbols.gsea_report_for_mCherry.tsv:md5,ce8792382ae299749445767ff16aaecc", - "treatment_mCherry_hND6__test.mh.all.v2022.1.Mm.symbols.gsea_report_for_hND6.tsv:md5,a4dcc9581c9c63d35ef32ee0df882074" + "treatment_mCherry_hND6_.mh.all.v2022.1.Mm.symbols.gsea_report_for_mCherry.tsv:md5,ce8792382ae299749445767ff16aaecc", + "treatment_mCherry_hND6_.mh.all.v2022.1.Mm.symbols.gsea_report_for_hND6.tsv:md5,a4dcc9581c9c63d35ef32ee0df882074" ], [ { - "id": "treatment_mCherry_hND6_sample_number_test", + "id": "treatment_mCherry_hND6_sample_number", + "method_de": "deseq2", + "method": "gsea", "variable": "treatment", "reference": "mCherry", "target": "hND6", - "blocking": "sample_number", - "method_de": "deseq2", - "method": "gsea" + "blocking": "sample_number" }, - "treatment_mCherry_hND6_sample_number_test.mh.all.v2022.1.Mm.symbols.gsea_report_for_mCherry.tsv:md5,ce8792382ae299749445767ff16aaecc", - "treatment_mCherry_hND6_sample_number_test.mh.all.v2022.1.Mm.symbols.gsea_report_for_hND6.tsv:md5,354a961c7e1417db2bf1f7e8d00c54f0" + "treatment_mCherry_hND6_sample_number.mh.all.v2022.1.Mm.symbols.gsea_report_for_mCherry.tsv:md5,ce8792382ae299749445767ff16aaecc", + "treatment_mCherry_hND6_sample_number.mh.all.v2022.1.Mm.symbols.gsea_report_for_hND6.tsv:md5,354a961c7e1417db2bf1f7e8d00c54f0" ], [ { - "id": "treatment_mCherry_hND6_sample_number_test", + "id": "treatment_mCherry_hND6_sample_number", + "method_de": "limma", + "method": "gsea", "variable": "treatment", "reference": "mCherry", "target": "hND6", - "blocking": "sample_number", - "method_de": "limma", - "method": "gsea" + "blocking": "sample_number" }, - "treatment_mCherry_hND6_sample_number_test.mh.all.v2022.1.Mm.symbols.gsea_report_for_mCherry.tsv:md5,ce8792382ae299749445767ff16aaecc", - "treatment_mCherry_hND6_sample_number_test.mh.all.v2022.1.Mm.symbols.gsea_report_for_hND6.tsv:md5,a4dcc9581c9c63d35ef32ee0df882074" + "treatment_mCherry_hND6_sample_number.mh.all.v2022.1.Mm.symbols.gsea_report_for_mCherry.tsv:md5,ce8792382ae299749445767ff16aaecc", + "treatment_mCherry_hND6_sample_number.mh.all.v2022.1.Mm.symbols.gsea_report_for_hND6.tsv:md5,a4dcc9581c9c63d35ef32ee0df882074" ] ], [ [ { - "id": "treatment_mCherry_hND6__test", + "id": "treatment_mCherry_hND6_", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -197,11 +196,11 @@ "method_de": "propd", "method": "grea" }, - "treatment_mCherry_hND6__test.grea.tsv:md5,786faeccf39926d2f7c980ef549a2697" + "treatment_mCherry_hND6_.grea.tsv:md5,786faeccf39926d2f7c980ef549a2697" ], [ { - "id": "treatment_mCherry_hND6_sample_number_test", + "id": "treatment_mCherry_hND6_sample_number", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -209,7 +208,7 @@ "method_de": "propd", "method": "grea" }, - "treatment_mCherry_hND6_sample_number_test.grea.tsv:md5,786faeccf39926d2f7c980ef549a2697" + "treatment_mCherry_hND6_sample_number.grea.tsv:md5,786faeccf39926d2f7c980ef549a2697" ] ], [ @@ -240,14 +239,14 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-01-24T15:12:40.203142527" + "timestamp": "2025-01-31T14:38:55.322768786" }, "propd + grea - mouse": { "content": [ [ [ { - "id": "treatment_mCherry_hND6__test", + "id": "treatment_mCherry_hND6_", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -255,11 +254,11 @@ "method_de": "propd", "method": "grea" }, - "treatment_mCherry_hND6__test.grea.tsv:md5,786faeccf39926d2f7c980ef549a2697" + "treatment_mCherry_hND6_.grea.tsv:md5,786faeccf39926d2f7c980ef549a2697" ], [ { - "id": "treatment_mCherry_hND6_sample_number_test", + "id": "treatment_mCherry_hND6_sample_number", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -267,7 +266,7 @@ "method_de": "propd", "method": "grea" }, - "treatment_mCherry_hND6_sample_number_test.grea.tsv:md5,786faeccf39926d2f7c980ef549a2697" + "treatment_mCherry_hND6_sample_number.grea.tsv:md5,786faeccf39926d2f7c980ef549a2697" ] ], { @@ -284,14 +283,14 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-01-24T15:10:22.944909501" + "timestamp": "2025-01-31T14:35:38.838594087" }, "deseq2 + gprofiler2 - mouse": { "content": [ [ [ { - "id": "treatment_mCherry_hND6__test", + "id": "treatment_mCherry_hND6_", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -301,11 +300,11 @@ "method_de": "deseq2", "method": "gprofiler2" }, - "treatment_mCherry_hND6__test.gprofiler2.all_enriched_pathways.tsv:md5,d586d92fb6cc3e41d493d14c4d9a7d92" + "treatment_mCherry_hND6_.gprofiler2.all_enriched_pathways.tsv:md5,10f7cef4ef0e1b0eab79818fdbaab9ad" ], [ { - "id": "treatment_mCherry_hND6_sample_number_test", + "id": "treatment_mCherry_hND6_sample_number", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -315,13 +314,13 @@ "method_de": "deseq2", "method": "gprofiler2" }, - "treatment_mCherry_hND6_sample_number_test.gprofiler2.all_enriched_pathways.tsv:md5,fa880c70d06f56d8dad0ac8078e6233c" + "treatment_mCherry_hND6_sample_number.gprofiler2.all_enriched_pathways.tsv:md5,7ac2c2f5c0ad3d72769419f065cb6ace" ] ], [ [ { - "id": "treatment_mCherry_hND6__test", + "id": "treatment_mCherry_hND6_", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -332,15 +331,15 @@ "method": "gprofiler2" }, [ - "treatment_mCherry_hND6__test.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,4c95059438af872253aa95a5ff127fca", - "treatment_mCherry_hND6__test.gprofiler2.GO:CC.sub_enriched_pathways.tsv:md5,b4e4009e067f723694efc1a46a609e2b", - "treatment_mCherry_hND6__test.gprofiler2.GO:MF.sub_enriched_pathways.tsv:md5,ece72606ce6d1d037cfd5f5b198233a8", - "treatment_mCherry_hND6__test.gprofiler2.REAC.sub_enriched_pathways.tsv:md5,dc7b6f67903e25076ab95a7e1bb39bbe" + "treatment_mCherry_hND6_.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,6047ffd74fe8a49db9b924485a441948", + "treatment_mCherry_hND6_.gprofiler2.GO:CC.sub_enriched_pathways.tsv:md5,891018299a66d62fbe979a56e9f31035", + "treatment_mCherry_hND6_.gprofiler2.GO:MF.sub_enriched_pathways.tsv:md5,46bb279062af777060495d56ac9767d7", + "treatment_mCherry_hND6_.gprofiler2.REAC.sub_enriched_pathways.tsv:md5,ca5e92673eb17242477e9c2787d68323" ] ], [ { - "id": "treatment_mCherry_hND6_sample_number_test", + "id": "treatment_mCherry_hND6_sample_number", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -351,17 +350,16 @@ "method": "gprofiler2" }, [ - "treatment_mCherry_hND6_sample_number_test.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,dc27af1c941636f8b03e8c8724773725", - "treatment_mCherry_hND6_sample_number_test.gprofiler2.GO:CC.sub_enriched_pathways.tsv:md5,09b7770d59d2efa8a58f300a16a41ae7", - "treatment_mCherry_hND6_sample_number_test.gprofiler2.GO:MF.sub_enriched_pathways.tsv:md5,a261d658ca1b1ec0511e55da734d7810", - "treatment_mCherry_hND6_sample_number_test.gprofiler2.KEGG.sub_enriched_pathways.tsv:md5,3cbdbbb1c5b232ab73d35d4a0953d19c", - "treatment_mCherry_hND6_sample_number_test.gprofiler2.REAC.sub_enriched_pathways.tsv:md5,8472cb5792bf7ec044bb95df356ad47e" + "treatment_mCherry_hND6_sample_number.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,f55e010f72ee9200624137f42e94a5e5", + "treatment_mCherry_hND6_sample_number.gprofiler2.GO:CC.sub_enriched_pathways.tsv:md5,5bb51d9184e7257ce6cdd0ce7db16923", + "treatment_mCherry_hND6_sample_number.gprofiler2.GO:MF.sub_enriched_pathways.tsv:md5,210e4b99919354c79b37e12c83fdeaa5", + "treatment_mCherry_hND6_sample_number.gprofiler2.REAC.sub_enriched_pathways.tsv:md5,d754c55c2a2a1b8acda1c663165b4d2b" ] ] ], [ - "treatment_mCherry_hND6__test.gprofiler2.gostplot.html", - "treatment_mCherry_hND6_sample_number_test.gprofiler2.gostplot.html" + "treatment_mCherry_hND6_.gprofiler2.gostplot.html", + "treatment_mCherry_hND6_sample_number.gprofiler2.gostplot.html" ], { "DIFFERENTIAL_FUNCTIONAL_ENRICHMENT:GPROFILER2_GOST": { @@ -379,7 +377,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-01-24T15:08:35.939943561" + "timestamp": "2025-01-31T14:32:57.471420763" }, "test gprofiler2 - mouse": { "content": [ @@ -393,7 +391,7 @@ "blocking": "batch", "method": "gprofiler2" }, - "Condition_genotype_WT_KO.gprofiler2.all_enriched_pathways.tsv:md5,1134a02ca061c463bcbff277eefbfb19" + "Condition_genotype_WT_KO.gprofiler2.all_enriched_pathways.tsv:md5,396712577c32213078d1604b1ba247de" ] ], [ @@ -407,15 +405,14 @@ "method": "gprofiler2" }, [ - "Condition_genotype_WT_KO.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,d527b94cdb160070bcaa0bfb0cecf914", - "Condition_genotype_WT_KO.gprofiler2.GO:CC.sub_enriched_pathways.tsv:md5,ef418c3f06d50446317928e37ec8ddfb", - "Condition_genotype_WT_KO.gprofiler2.GO:MF.sub_enriched_pathways.tsv:md5,e460d4917feb0b64d334a528f59e0731", - "Condition_genotype_WT_KO.gprofiler2.HP.sub_enriched_pathways.tsv:md5,865d8f092503552831c51d775a98c6eb", - "Condition_genotype_WT_KO.gprofiler2.KEGG.sub_enriched_pathways.tsv:md5,413724002abe683f376ea914d4f21ade", - "Condition_genotype_WT_KO.gprofiler2.MIRNA.sub_enriched_pathways.tsv:md5,fce81051d7af955ddb2925ba2da9ff57", - "Condition_genotype_WT_KO.gprofiler2.REAC.sub_enriched_pathways.tsv:md5,e89e1876698ea644671a0720c85f4dbb", - "Condition_genotype_WT_KO.gprofiler2.TF.sub_enriched_pathways.tsv:md5,e272217ec7fcf01ea463ab8bcc8335cf", - "Condition_genotype_WT_KO.gprofiler2.WP.sub_enriched_pathways.tsv:md5,fdd1efa836d85bb127e933e925290cba" + "Condition_genotype_WT_KO.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,d6bebdcb2401a7f7de0ec42ad2f4521d", + "Condition_genotype_WT_KO.gprofiler2.GO:CC.sub_enriched_pathways.tsv:md5,98a49b69f8b724d88d6367dea494ca53", + "Condition_genotype_WT_KO.gprofiler2.GO:MF.sub_enriched_pathways.tsv:md5,39ce8238319df47708df78b1c461a89d", + "Condition_genotype_WT_KO.gprofiler2.HP.sub_enriched_pathways.tsv:md5,616f3a5d19844001bb8aac38049e987a", + "Condition_genotype_WT_KO.gprofiler2.MIRNA.sub_enriched_pathways.tsv:md5,486ed1510dc8bba867686b021d6e6339", + "Condition_genotype_WT_KO.gprofiler2.REAC.sub_enriched_pathways.tsv:md5,3571ac765c47e1c38c63c463465f2a1e", + "Condition_genotype_WT_KO.gprofiler2.TF.sub_enriched_pathways.tsv:md5,032491e63bb381cc9a4d7740473efc5b", + "Condition_genotype_WT_KO.gprofiler2.WP.sub_enriched_pathways.tsv:md5,e99c42df912a9ee75c7197f92d615979" ] ] ], @@ -437,36 +434,36 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-01-24T15:07:42.734133807" + "timestamp": "2025-01-31T14:31:40.671620493" }, "deseq2 + gsea - mouse": { "content": [ [ [ { - "id": "treatment_mCherry_hND6__test", + "id": "treatment_mCherry_hND6_", + "method_de": "deseq2", + "method": "gsea", "variable": "treatment", "reference": "mCherry", "target": "hND6", - "blocking": "", - "method_de": "deseq2", - "method": "gsea" + "blocking": "" }, - "treatment_mCherry_hND6__test.mh.all.v2022.1.Mm.symbols.gsea_report_for_mCherry.tsv:md5,ce8792382ae299749445767ff16aaecc", - "treatment_mCherry_hND6__test.mh.all.v2022.1.Mm.symbols.gsea_report_for_hND6.tsv:md5,354a961c7e1417db2bf1f7e8d00c54f0" + "treatment_mCherry_hND6_.mh.all.v2022.1.Mm.symbols.gsea_report_for_mCherry.tsv:md5,ce8792382ae299749445767ff16aaecc", + "treatment_mCherry_hND6_.mh.all.v2022.1.Mm.symbols.gsea_report_for_hND6.tsv:md5,354a961c7e1417db2bf1f7e8d00c54f0" ], [ { - "id": "treatment_mCherry_hND6_sample_number_test", + "id": "treatment_mCherry_hND6_sample_number", + "method_de": "deseq2", + "method": "gsea", "variable": "treatment", "reference": "mCherry", "target": "hND6", - "blocking": "sample_number", - "method_de": "deseq2", - "method": "gsea" + "blocking": "sample_number" }, - "treatment_mCherry_hND6_sample_number_test.mh.all.v2022.1.Mm.symbols.gsea_report_for_mCherry.tsv:md5,ce8792382ae299749445767ff16aaecc", - "treatment_mCherry_hND6_sample_number_test.mh.all.v2022.1.Mm.symbols.gsea_report_for_hND6.tsv:md5,354a961c7e1417db2bf1f7e8d00c54f0" + "treatment_mCherry_hND6_sample_number.mh.all.v2022.1.Mm.symbols.gsea_report_for_mCherry.tsv:md5,ce8792382ae299749445767ff16aaecc", + "treatment_mCherry_hND6_sample_number.mh.all.v2022.1.Mm.symbols.gsea_report_for_hND6.tsv:md5,354a961c7e1417db2bf1f7e8d00c54f0" ] ], { @@ -488,7 +485,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-01-24T15:09:55.875311067" + "timestamp": "2025-01-31T14:34:55.565980336" }, "stub": { "content": [ From ed9ecd060a1d296f572fe995b9c3282ef208769f Mon Sep 17 00:00:00 2001 From: Suzanne Jin Date: Fri, 31 Jan 2025 16:00:24 +0000 Subject: [PATCH 05/15] [gprofiler2] add option to specify the database archive --- .../nf-core/gprofiler2/gost/templates/gprofiler2_gost.R | 7 +++++-- modules/nf-core/gprofiler2/gost/tests/main.nf.test | 3 ++- modules/nf-core/gprofiler2/gost/tests/nextflow.config | 2 +- 3 files changed, 8 insertions(+), 4 deletions(-) diff --git a/modules/nf-core/gprofiler2/gost/templates/gprofiler2_gost.R b/modules/nf-core/gprofiler2/gost/templates/gprofiler2_gost.R index 0e2c0f1e621..b7665610e3d 100644 --- a/modules/nf-core/gprofiler2/gost/templates/gprofiler2_gost.R +++ b/modules/nf-core/gprofiler2/gost/templates/gprofiler2_gost.R @@ -139,7 +139,8 @@ opt <- list( domain_scope = 'annotated', min_diff = 1, round_digits = -1, - palette_name = 'Blues' + palette_name = 'Blues', + archive = 'gprofiler' ) opt_types <- lapply(opt, class) @@ -182,6 +183,8 @@ for (file_input in c('de_file')) { } } +print(opt) + ################################################ ################################################ ## Finish loading libraries ## @@ -235,7 +238,7 @@ if (nrow(de.genes) > 0) { } else if (!is.null(opt\$organism)) { # Next, check if organism was provided. Get the GMT file from gprofiler and save both the full file as well as the filtered one to metadata - gmt_url <- paste0("https://biit.cs.ut.ee/gprofiler//static/gprofiler_full_", opt\$organism, ".ENSG.gmt") + gmt_url <- paste0("https://biit.cs.ut.ee/", opt\$archive, "//static/gprofiler_full_", opt\$organism, ".ENSG.gmt") tryCatch( { gmt_path <- paste0("gprofiler_full_", opt\$organism, ".ENSG.gmt") diff --git a/modules/nf-core/gprofiler2/gost/tests/main.nf.test b/modules/nf-core/gprofiler2/gost/tests/main.nf.test index e2528ef2fe0..03bbaf64fe4 100644 --- a/modules/nf-core/gprofiler2/gost/tests/main.nf.test +++ b/modules/nf-core/gprofiler2/gost/tests/main.nf.test @@ -46,7 +46,8 @@ nextflow_process { ((params.gprofiler2_token == null) ? '' : "--token \"${params.gprofiler2_token}\""), ((params.gprofiler2_organism == null) ? '' : "--organism \"${params.gprofiler2_organism}\""), ((params.gprofiler2_background_column == null) ? '' : "--background_column \"${params.gprofiler2_background_column}\""), - ((params.gprofiler2_sources == null) ? '' : "--sources \"${params.gprofiler2_sources}\"") + ((params.gprofiler2_sources == null) ? '' : "--sources \"${params.gprofiler2_sources}\""), + "--archive gprofiler_archive3/e111_eg58_p18" ].join(' ').trim() } process { diff --git a/modules/nf-core/gprofiler2/gost/tests/nextflow.config b/modules/nf-core/gprofiler2/gost/tests/nextflow.config index 1a77344d7ff..ad3d36ef5c9 100644 --- a/modules/nf-core/gprofiler2/gost/tests/nextflow.config +++ b/modules/nf-core/gprofiler2/gost/tests/nextflow.config @@ -1,3 +1,3 @@ process { ext.args = params.module_args -} \ No newline at end of file +} From 24429b59b801e5b40042257aef78494610733406 Mon Sep 17 00:00:00 2001 From: Suzanne Jin Date: Tue, 4 Feb 2025 09:46:15 +0000 Subject: [PATCH 06/15] [gsea] remove default seed set in gsea module --- modules/nf-core/gprofiler2/gost/templates/gprofiler2_gost.R | 2 -- modules/nf-core/gsea/gsea/main.nf | 1 - 2 files changed, 3 deletions(-) diff --git a/modules/nf-core/gprofiler2/gost/templates/gprofiler2_gost.R b/modules/nf-core/gprofiler2/gost/templates/gprofiler2_gost.R index b7665610e3d..ce50aa38d41 100644 --- a/modules/nf-core/gprofiler2/gost/templates/gprofiler2_gost.R +++ b/modules/nf-core/gprofiler2/gost/templates/gprofiler2_gost.R @@ -183,8 +183,6 @@ for (file_input in c('de_file')) { } } -print(opt) - ################################################ ################################################ ## Finish loading libraries ## diff --git a/modules/nf-core/gsea/gsea/main.nf b/modules/nf-core/gsea/gsea/main.nf index 7813308fa6f..254d68d39d1 100644 --- a/modules/nf-core/gsea/gsea/main.nf +++ b/modules/nf-core/gsea/gsea/main.nf @@ -45,7 +45,6 @@ process GSEA_GSEA { def rpt_label = prefix.replaceAll('\\.$', '') // Remove any trailing dots from prefix when passed as report label, so GSEA doesn't produce double-dotted top-level outputs def chip_command = chip ? "-chip $chip -collapse true" : '' def VERSION = '4.3.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. - // if (!(args ==~ /.*-rnd_seed.*/)) {args += " -rnd_seed 10"} // unable this for the moment, until a global seed option is set for differentialabundance pipeline """ # Run GSEA From a227160073f6dc5aba8d5a2b2ae6c5bc9892ae5b Mon Sep 17 00:00:00 2001 From: Suzanne Jin Date: Tue, 4 Feb 2025 10:58:51 +0000 Subject: [PATCH 07/15] change(abundance_differential_filter): use groupTuple for ch_variance_stabilised_matrix --- .../nf-core/abundance_differential_filter/main.nf | 13 +++---------- 1 file changed, 3 insertions(+), 10 deletions(-) diff --git a/subworkflows/nf-core/abundance_differential_filter/main.nf b/subworkflows/nf-core/abundance_differential_filter/main.nf index 88cbbec4112..9010ae73ecf 100644 --- a/subworkflows/nf-core/abundance_differential_filter/main.nf +++ b/subworkflows/nf-core/abundance_differential_filter/main.nf @@ -126,16 +126,9 @@ workflow ABUNDANCE_DIFFERENTIAL_FILTER { .mix(LIMMA_DIFFERENTIAL.out.model) ch_variance_stabilised_matrix = DESEQ2_NORM.out.rlog_counts.ifEmpty([[],[]]) - .combine(DESEQ2_NORM.out.vst_counts.ifEmpty([[],[]])) - .map { meta_rlog, rlog, meta_vst, vst -> - if (meta_rlog == meta_vst && meta_rlog != []) { - return [meta_rlog, [rlog, vst]] - } else if (meta_rlog != [] && meta_vst == []) { - return [meta_rlog, [rlog]] - } else if (meta_rlog == [] && meta_vst != []) { - return [meta_vst, [vst]] - } - } + .mix(DESEQ2_NORM.out.vst_counts.ifEmpty([[],[]])) + .groupTuple() + .filter{ meta, files -> meta != [] } ch_versions = DESEQ2_DIFFERENTIAL.out.versions .mix(LIMMA_DIFFERENTIAL.out.versions) From e77e7fa9112aeb1aa82d4d95b55b5cc517a09137 Mon Sep 17 00:00:00 2001 From: Suzanne Jin Date: Tue, 4 Feb 2025 15:05:42 +0000 Subject: [PATCH 08/15] change(differential and functional subworkflows): add back mergeMap and update snapshots --- .../abundance_differential_filter/main.nf | 8 +- .../tests/main.nf.test.snap | 292 +++++++++--------- .../main.nf | 8 +- .../tests/main.nf.test.snap | 199 ++++++------ 4 files changed, 261 insertions(+), 246 deletions(-) diff --git a/subworkflows/nf-core/abundance_differential_filter/main.nf b/subworkflows/nf-core/abundance_differential_filter/main.nf index 9010ae73ecf..d2617fb591f 100644 --- a/subworkflows/nf-core/abundance_differential_filter/main.nf +++ b/subworkflows/nf-core/abundance_differential_filter/main.nf @@ -9,6 +9,12 @@ include { DESEQ2_DIFFERENTIAL as DESEQ2_NORM } from '../../../modules/nf-core/d include { PROPR_PROPD } from '../../../modules/nf-core/propr/propd/main' include { CUSTOM_FILTERDIFFERENTIALTABLE } from '../../../modules/nf-core/custom/filterdifferentialtable/main' +// Combine meta maps, including merging non-identical values of shared keys (e.g. 'id') +def mergeMaps(meta, meta2){ + (meta + meta2).collectEntries { k, v -> + meta[k] && meta[k] != v ? [k, "${meta[k]}_${v}"] : [k, v] + } +} workflow ABUNDANCE_DIFFERENTIAL_FILTER { take: @@ -25,7 +31,7 @@ workflow ABUNDANCE_DIFFERENTIAL_FILTER { // Set up how the channels crossed below will be used to generate channels for processing def criteria = multiMapCriteria { meta_input, abundance, analysis_method, fc_threshold, stat_threshold, meta_exp, samplesheet, meta_contrasts, variable, reference, target -> - def meta_for_diff = meta_input + meta_contrasts + [ 'method': analysis_method ] + def meta_for_diff = mergeMaps(meta_contrasts, meta_input) + [ 'method': analysis_method ] def meta_input_new = meta_input + [ 'method': analysis_method ] samples_and_matrix: [ meta_input_new, samplesheet, abundance ] diff --git a/subworkflows/nf-core/abundance_differential_filter/tests/main.nf.test.snap b/subworkflows/nf-core/abundance_differential_filter/tests/main.nf.test.snap index a03d01510b7..c1b1f0ec90b 100644 --- a/subworkflows/nf-core/abundance_differential_filter/tests/main.nf.test.snap +++ b/subworkflows/nf-core/abundance_differential_filter/tests/main.nf.test.snap @@ -4,19 +4,19 @@ [ [ { - "id": "diagnosis_normal_uremia", + "id": "diagnosis_normal_uremia_test", "variable": "diagnosis", "reference": "normal", "target": "uremia", "method": "limma" }, - "diagnosis_normal_uremia_limma.limma.results.tsv:md5,4f0944b54b3ab7aa6ded5dd4b4e82802" + "diagnosis_normal_uremia_test_limma.limma.results.tsv:md5,4f0944b54b3ab7aa6ded5dd4b4e82802" ] ], [ [ { - "id": "diagnosis_normal_uremia", + "id": "diagnosis_normal_uremia_test", "variable": "diagnosis", "reference": "normal", "target": "uremia", @@ -24,22 +24,22 @@ "fc_threshold": 1.5, "stat_threshold": 0.05 }, - "diagnosis_normal_uremia_filtered.tsv:md5,a971455ece4ae3c3ab902407b36fc6a5" + "diagnosis_normal_uremia_test_filtered.tsv:md5,a971455ece4ae3c3ab902407b36fc6a5" ] ], [ - + ], [ [ { - "id": "diagnosis_normal_uremia", + "id": "diagnosis_normal_uremia_test", "variable": "diagnosis", "reference": "normal", "target": "uremia", "method": "limma" }, - "diagnosis_normal_uremia_limma.limma.model.txt:md5,70b000f632b8bdba4917046362dd876b" + "diagnosis_normal_uremia_test_limma.limma.model.txt:md5,70b000f632b8bdba4917046362dd876b" ] ], [ @@ -50,60 +50,60 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-01-31T13:51:00.356867156" + "timestamp": "2025-02-04T13:54:29.394126445" }, "deseq2 and limma - mouse - basic": { "content": [ [ [ { - "id": "treatment_mCherry_hND6_", + "id": "treatment_mCherry_hND6__test", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "", "method": "deseq2" }, - "treatment_mCherry_hND6__deseq2.deseq2.results.tsv:md5,791cdba2615a445cded13cae95df73ef" + "treatment_mCherry_hND6__test_deseq2.deseq2.results.tsv:md5,791cdba2615a445cded13cae95df73ef" ], [ { - "id": "treatment_mCherry_hND6_", + "id": "treatment_mCherry_hND6__test", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "", "method": "limma" }, - "treatment_mCherry_hND6__limma_voom.limma.results.tsv:md5,ff36827b7869a8a3c3c905efedcafc93" + "treatment_mCherry_hND6__test_limma_voom.limma.results.tsv:md5,ff36827b7869a8a3c3c905efedcafc93" ], [ { - "id": "treatment_mCherry_hND6_sample_number", + "id": "treatment_mCherry_hND6_sample_number_test", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "sample_number", "method": "deseq2" }, - "treatment_mCherry_hND6_sample_number_deseq2.deseq2.results.tsv:md5,2438053a4bdc869f467a12d3c22c7ba7" + "treatment_mCherry_hND6_sample_number_test_deseq2.deseq2.results.tsv:md5,2438053a4bdc869f467a12d3c22c7ba7" ], [ { - "id": "treatment_mCherry_hND6_sample_number", + "id": "treatment_mCherry_hND6_sample_number_test", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "sample_number", "method": "limma" }, - "treatment_mCherry_hND6_sample_number_limma_voom.limma.results.tsv:md5,5f34e79dbcb5ba1908d797548921d7fc" + "treatment_mCherry_hND6_sample_number_test_limma_voom.limma.results.tsv:md5,5f34e79dbcb5ba1908d797548921d7fc" ] ], [ [ { - "id": "treatment_mCherry_hND6_", + "id": "treatment_mCherry_hND6__test", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -112,11 +112,11 @@ "fc_threshold": 1.5, "stat_threshold": 0.05 }, - "treatment_mCherry_hND6__filtered.tsv:md5,7829ead408f4c9cad4277598a231c494" + "treatment_mCherry_hND6__test_filtered.tsv:md5,7829ead408f4c9cad4277598a231c494" ], [ { - "id": "treatment_mCherry_hND6_", + "id": "treatment_mCherry_hND6__test", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -125,11 +125,11 @@ "fc_threshold": 1.5, "stat_threshold": 0.05 }, - "treatment_mCherry_hND6__filtered.tsv:md5,0bfc9215edc6aad064c3ce6abc81bfce" + "treatment_mCherry_hND6__test_filtered.tsv:md5,0bfc9215edc6aad064c3ce6abc81bfce" ], [ { - "id": "treatment_mCherry_hND6_sample_number", + "id": "treatment_mCherry_hND6_sample_number_test", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -138,11 +138,11 @@ "fc_threshold": 1.5, "stat_threshold": 0.05 }, - "treatment_mCherry_hND6_sample_number_filtered.tsv:md5,8b084475c9e7e1b34a510a73b613ff39" + "treatment_mCherry_hND6_sample_number_test_filtered.tsv:md5,8b084475c9e7e1b34a510a73b613ff39" ], [ { - "id": "treatment_mCherry_hND6_sample_number", + "id": "treatment_mCherry_hND6_sample_number_test", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -151,7 +151,7 @@ "fc_threshold": 1.5, "stat_threshold": 0.05 }, - "treatment_mCherry_hND6_sample_number_filtered.tsv:md5,0bfc9215edc6aad064c3ce6abc81bfce" + "treatment_mCherry_hND6_sample_number_test_filtered.tsv:md5,0bfc9215edc6aad064c3ce6abc81bfce" ] ], [ @@ -184,47 +184,47 @@ [ [ { - "id": "treatment_mCherry_hND6_", + "id": "treatment_mCherry_hND6__test", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "", "method": "deseq2" }, - "treatment_mCherry_hND6__deseq2.deseq2.model.txt:md5,d2113d82b76046c319e6602da2ad74d6" + "treatment_mCherry_hND6__test_deseq2.deseq2.model.txt:md5,d2113d82b76046c319e6602da2ad74d6" ], [ { - "id": "treatment_mCherry_hND6_", + "id": "treatment_mCherry_hND6__test", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "", "method": "limma" }, - "treatment_mCherry_hND6__limma_voom.limma.model.txt:md5,d2113d82b76046c319e6602da2ad74d6" + "treatment_mCherry_hND6__test_limma_voom.limma.model.txt:md5,d2113d82b76046c319e6602da2ad74d6" ], [ { - "id": "treatment_mCherry_hND6_sample_number", + "id": "treatment_mCherry_hND6_sample_number_test", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "sample_number", "method": "deseq2" }, - "treatment_mCherry_hND6_sample_number_deseq2.deseq2.model.txt:md5,fa05126a58cb67c107d45426b0bdea83" + "treatment_mCherry_hND6_sample_number_test_deseq2.deseq2.model.txt:md5,fa05126a58cb67c107d45426b0bdea83" ], [ { - "id": "treatment_mCherry_hND6_sample_number", + "id": "treatment_mCherry_hND6_sample_number_test", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "sample_number", "method": "limma" }, - "treatment_mCherry_hND6_sample_number_limma_voom.limma.model.txt:md5,3b96713b4e3f027b0347859f02a9038d" + "treatment_mCherry_hND6_sample_number_test_limma_voom.limma.model.txt:md5,3b96713b4e3f027b0347859f02a9038d" ] ], [ @@ -238,14 +238,14 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-01-31T13:53:24.035095649" + "timestamp": "2025-02-04T13:56:48.852994235" }, "limma - voom": { "content": [ [ [ { - "id": "treatment_mCherry_hND6_", + "id": "treatment_mCherry_hND6__test", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -254,11 +254,11 @@ "fc_threshold": 1.5, "stat_threshold": 0.05 }, - "treatment_mCherry_hND6__filtered.tsv:md5,0bfc9215edc6aad064c3ce6abc81bfce" + "treatment_mCherry_hND6__test_filtered.tsv:md5,0bfc9215edc6aad064c3ce6abc81bfce" ], [ { - "id": "treatment_mCherry_hND6_sample_number", + "id": "treatment_mCherry_hND6_sample_number_test", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -267,7 +267,7 @@ "fc_threshold": 1.5, "stat_threshold": 0.05 }, - "treatment_mCherry_hND6_sample_number_filtered.tsv:md5,0bfc9215edc6aad064c3ce6abc81bfce" + "treatment_mCherry_hND6_sample_number_test_filtered.tsv:md5,0bfc9215edc6aad064c3ce6abc81bfce" ] ], [ @@ -282,25 +282,25 @@ [ [ { - "id": "treatment_mCherry_hND6_", + "id": "treatment_mCherry_hND6__test", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "", "method": "limma" }, - "treatment_mCherry_hND6__limma_voom.limma.model.txt:md5,d2113d82b76046c319e6602da2ad74d6" + "treatment_mCherry_hND6__test_limma_voom.limma.model.txt:md5,d2113d82b76046c319e6602da2ad74d6" ], [ { - "id": "treatment_mCherry_hND6_sample_number", + "id": "treatment_mCherry_hND6_sample_number_test", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "sample_number", "method": "limma" }, - "treatment_mCherry_hND6_sample_number_limma_voom.limma.model.txt:md5,3b96713b4e3f027b0347859f02a9038d" + "treatment_mCherry_hND6_sample_number_test_limma_voom.limma.model.txt:md5,3b96713b4e3f027b0347859f02a9038d" ] ], [ @@ -312,82 +312,82 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-01-31T13:51:18.880578932" + "timestamp": "2025-02-04T13:54:49.182493737" }, "deseq2 + limma-voom + propd - mouse - basic": { "content": [ [ [ { - "id": "treatment_mCherry_hND6_", + "id": "treatment_mCherry_hND6__test", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "", "method": "deseq2" }, - "treatment_mCherry_hND6__deseq2.deseq2.results.tsv:md5,791cdba2615a445cded13cae95df73ef" + "treatment_mCherry_hND6__test_deseq2.deseq2.results.tsv:md5,791cdba2615a445cded13cae95df73ef" ], [ { - "id": "treatment_mCherry_hND6_", + "id": "treatment_mCherry_hND6__test", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "", "method": "limma" }, - "treatment_mCherry_hND6__limma_voom.limma.results.tsv:md5,ff36827b7869a8a3c3c905efedcafc93" + "treatment_mCherry_hND6__test_limma_voom.limma.results.tsv:md5,ff36827b7869a8a3c3c905efedcafc93" ], [ { - "id": "treatment_mCherry_hND6_", + "id": "treatment_mCherry_hND6__test", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "", "method": "propd" }, - "treatment_mCherry_hND6__propd.propd.genewise.tsv:md5,bdc19a4b7430f248cd332287b630c872" + "treatment_mCherry_hND6__test_propd.propd.genewise.tsv:md5,bdc19a4b7430f248cd332287b630c872" ], [ { - "id": "treatment_mCherry_hND6_sample_number", + "id": "treatment_mCherry_hND6_sample_number_test", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "sample_number", "method": "deseq2" }, - "treatment_mCherry_hND6_sample_number_deseq2.deseq2.results.tsv:md5,2438053a4bdc869f467a12d3c22c7ba7" + "treatment_mCherry_hND6_sample_number_test_deseq2.deseq2.results.tsv:md5,2438053a4bdc869f467a12d3c22c7ba7" ], [ { - "id": "treatment_mCherry_hND6_sample_number", + "id": "treatment_mCherry_hND6_sample_number_test", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "sample_number", "method": "limma" }, - "treatment_mCherry_hND6_sample_number_limma_voom.limma.results.tsv:md5,5f34e79dbcb5ba1908d797548921d7fc" + "treatment_mCherry_hND6_sample_number_test_limma_voom.limma.results.tsv:md5,5f34e79dbcb5ba1908d797548921d7fc" ], [ { - "id": "treatment_mCherry_hND6_sample_number", + "id": "treatment_mCherry_hND6_sample_number_test", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "sample_number", "method": "propd" }, - "treatment_mCherry_hND6_sample_number_propd.propd.genewise.tsv:md5,bdc19a4b7430f248cd332287b630c872" + "treatment_mCherry_hND6_sample_number_test_propd.propd.genewise.tsv:md5,bdc19a4b7430f248cd332287b630c872" ] ], [ [ { - "id": "treatment_mCherry_hND6_", + "id": "treatment_mCherry_hND6__test", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -396,11 +396,11 @@ "fc_threshold": 1.5, "stat_threshold": 0.05 }, - "treatment_mCherry_hND6__filtered.tsv:md5,7829ead408f4c9cad4277598a231c494" + "treatment_mCherry_hND6__test_filtered.tsv:md5,7829ead408f4c9cad4277598a231c494" ], [ { - "id": "treatment_mCherry_hND6_", + "id": "treatment_mCherry_hND6__test", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -409,11 +409,11 @@ "fc_threshold": 1.5, "stat_threshold": 0.05 }, - "treatment_mCherry_hND6__filtered.tsv:md5,0bfc9215edc6aad064c3ce6abc81bfce" + "treatment_mCherry_hND6__test_filtered.tsv:md5,0bfc9215edc6aad064c3ce6abc81bfce" ], [ { - "id": "treatment_mCherry_hND6_", + "id": "treatment_mCherry_hND6__test", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -422,11 +422,11 @@ "fc_threshold": 1.5, "stat_threshold": 100 }, - "treatment_mCherry_hND6__filtered.tsv:md5,432b2ba4e63fd8f7e2aee74e5b71b0a5" + "treatment_mCherry_hND6__test_filtered.tsv:md5,432b2ba4e63fd8f7e2aee74e5b71b0a5" ], [ { - "id": "treatment_mCherry_hND6_sample_number", + "id": "treatment_mCherry_hND6_sample_number_test", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -435,11 +435,11 @@ "fc_threshold": 1.5, "stat_threshold": 0.05 }, - "treatment_mCherry_hND6_sample_number_filtered.tsv:md5,8b084475c9e7e1b34a510a73b613ff39" + "treatment_mCherry_hND6_sample_number_test_filtered.tsv:md5,8b084475c9e7e1b34a510a73b613ff39" ], [ { - "id": "treatment_mCherry_hND6_sample_number", + "id": "treatment_mCherry_hND6_sample_number_test", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -448,11 +448,11 @@ "fc_threshold": 1.5, "stat_threshold": 0.05 }, - "treatment_mCherry_hND6_sample_number_filtered.tsv:md5,0bfc9215edc6aad064c3ce6abc81bfce" + "treatment_mCherry_hND6_sample_number_test_filtered.tsv:md5,0bfc9215edc6aad064c3ce6abc81bfce" ], [ { - "id": "treatment_mCherry_hND6_sample_number", + "id": "treatment_mCherry_hND6_sample_number_test", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -461,31 +461,31 @@ "fc_threshold": 1.5, "stat_threshold": 100 }, - "treatment_mCherry_hND6_sample_number_filtered.tsv:md5,432b2ba4e63fd8f7e2aee74e5b71b0a5" + "treatment_mCherry_hND6_sample_number_test_filtered.tsv:md5,432b2ba4e63fd8f7e2aee74e5b71b0a5" ] ], [ [ { - "id": "treatment_mCherry_hND6_", + "id": "treatment_mCherry_hND6__test", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "", "method": "propd" }, - "treatment_mCherry_hND6__propd.propd.adjacency.csv:md5,3a947ffd8172990c6207aa7561a41cb8" + "treatment_mCherry_hND6__test_propd.propd.adjacency.csv:md5,3a947ffd8172990c6207aa7561a41cb8" ], [ { - "id": "treatment_mCherry_hND6_sample_number", + "id": "treatment_mCherry_hND6_sample_number_test", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "sample_number", "method": "propd" }, - "treatment_mCherry_hND6_sample_number_propd.propd.adjacency.csv:md5,3a947ffd8172990c6207aa7561a41cb8" + "treatment_mCherry_hND6_sample_number_test_propd.propd.adjacency.csv:md5,3a947ffd8172990c6207aa7561a41cb8" ] ], [ @@ -518,47 +518,47 @@ [ [ { - "id": "treatment_mCherry_hND6_", + "id": "treatment_mCherry_hND6__test", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "", "method": "deseq2" }, - "treatment_mCherry_hND6__deseq2.deseq2.model.txt:md5,d2113d82b76046c319e6602da2ad74d6" + "treatment_mCherry_hND6__test_deseq2.deseq2.model.txt:md5,d2113d82b76046c319e6602da2ad74d6" ], [ { - "id": "treatment_mCherry_hND6_", + "id": "treatment_mCherry_hND6__test", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "", "method": "limma" }, - "treatment_mCherry_hND6__limma_voom.limma.model.txt:md5,d2113d82b76046c319e6602da2ad74d6" + "treatment_mCherry_hND6__test_limma_voom.limma.model.txt:md5,d2113d82b76046c319e6602da2ad74d6" ], [ { - "id": "treatment_mCherry_hND6_sample_number", + "id": "treatment_mCherry_hND6_sample_number_test", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "sample_number", "method": "deseq2" }, - "treatment_mCherry_hND6_sample_number_deseq2.deseq2.model.txt:md5,fa05126a58cb67c107d45426b0bdea83" + "treatment_mCherry_hND6_sample_number_test_deseq2.deseq2.model.txt:md5,fa05126a58cb67c107d45426b0bdea83" ], [ { - "id": "treatment_mCherry_hND6_sample_number", + "id": "treatment_mCherry_hND6_sample_number_test", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "sample_number", "method": "limma" }, - "treatment_mCherry_hND6_sample_number_limma_voom.limma.model.txt:md5,3b96713b4e3f027b0347859f02a9038d" + "treatment_mCherry_hND6_sample_number_test_limma_voom.limma.model.txt:md5,3b96713b4e3f027b0347859f02a9038d" ] ], [ @@ -574,7 +574,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-01-31T13:54:15.858310302" + "timestamp": "2025-02-04T13:57:45.650163566" }, "stub": { "content": [ @@ -582,31 +582,31 @@ "0": [ [ { - "id": "treatment_mCherry_hND6_", + "id": "treatment_mCherry_hND6__test", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "", "method": "deseq2" }, - "treatment_mCherry_hND6_.deseq2.results.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + "treatment_mCherry_hND6__test.deseq2.results.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ], [ { - "id": "treatment_mCherry_hND6_sample_number", + "id": "treatment_mCherry_hND6_sample_number_test", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "sample_number", "method": "deseq2" }, - "treatment_mCherry_hND6_sample_number.deseq2.results.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + "treatment_mCherry_hND6_sample_number_test.deseq2.results.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "1": [ [ { - "id": "treatment_mCherry_hND6_", + "id": "treatment_mCherry_hND6__test", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -615,11 +615,11 @@ "fc_threshold": 1.5, "stat_threshold": 0.05 }, - "treatment_mCherry_hND6__filtered.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + "treatment_mCherry_hND6__test_filtered.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ], [ { - "id": "treatment_mCherry_hND6_sample_number", + "id": "treatment_mCherry_hND6_sample_number_test", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -628,11 +628,11 @@ "fc_threshold": 1.5, "stat_threshold": 0.05 }, - "treatment_mCherry_hND6_sample_number_filtered.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + "treatment_mCherry_hND6_sample_number_test_filtered.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "2": [ - + ], "3": [ [ @@ -657,25 +657,25 @@ "5": [ [ { - "id": "treatment_mCherry_hND6_", + "id": "treatment_mCherry_hND6__test", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "", "method": "deseq2" }, - "treatment_mCherry_hND6_.deseq2.model.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + "treatment_mCherry_hND6__test.deseq2.model.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ], [ { - "id": "treatment_mCherry_hND6_sample_number", + "id": "treatment_mCherry_hND6_sample_number_test", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "sample_number", "method": "deseq2" }, - "treatment_mCherry_hND6_sample_number.deseq2.model.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + "treatment_mCherry_hND6_sample_number_test.deseq2.model.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "6": [ @@ -683,30 +683,30 @@ "versions.yml:md5,05e3901f6d78f8839a7e07f422e9bc03" ], "adjacency": [ - + ], "model": [ [ { - "id": "treatment_mCherry_hND6_", + "id": "treatment_mCherry_hND6__test", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "", "method": "deseq2" }, - "treatment_mCherry_hND6_.deseq2.model.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + "treatment_mCherry_hND6__test.deseq2.model.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ], [ { - "id": "treatment_mCherry_hND6_sample_number", + "id": "treatment_mCherry_hND6_sample_number_test", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "sample_number", "method": "deseq2" }, - "treatment_mCherry_hND6_sample_number.deseq2.model.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + "treatment_mCherry_hND6_sample_number_test.deseq2.model.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "normalised_matrix": [ @@ -721,31 +721,31 @@ "results_genewise": [ [ { - "id": "treatment_mCherry_hND6_", + "id": "treatment_mCherry_hND6__test", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "", "method": "deseq2" }, - "treatment_mCherry_hND6_.deseq2.results.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + "treatment_mCherry_hND6__test.deseq2.results.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ], [ { - "id": "treatment_mCherry_hND6_sample_number", + "id": "treatment_mCherry_hND6_sample_number_test", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "sample_number", "method": "deseq2" }, - "treatment_mCherry_hND6_sample_number.deseq2.results.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + "treatment_mCherry_hND6_sample_number_test.deseq2.results.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "results_genewise_filtered": [ [ { - "id": "treatment_mCherry_hND6_", + "id": "treatment_mCherry_hND6__test", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -754,11 +754,11 @@ "fc_threshold": 1.5, "stat_threshold": 0.05 }, - "treatment_mCherry_hND6__filtered.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + "treatment_mCherry_hND6__test_filtered.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ], [ { - "id": "treatment_mCherry_hND6_sample_number", + "id": "treatment_mCherry_hND6_sample_number_test", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -767,7 +767,7 @@ "fc_threshold": 1.5, "stat_threshold": 0.05 }, - "treatment_mCherry_hND6_sample_number_filtered.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + "treatment_mCherry_hND6_sample_number_test_filtered.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "variance_stabilised_matrix": [ @@ -791,38 +791,38 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-01-31T13:54:38.936440968" + "timestamp": "2025-02-04T13:58:07.872952803" }, "deseq2 - mouse - basic": { "content": [ [ [ { - "id": "treatment_mCherry_hND6_", + "id": "treatment_mCherry_hND6__test", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "", "method": "deseq2" }, - "treatment_mCherry_hND6__deseq2.deseq2.results.tsv:md5,791cdba2615a445cded13cae95df73ef" + "treatment_mCherry_hND6__test_deseq2.deseq2.results.tsv:md5,791cdba2615a445cded13cae95df73ef" ], [ { - "id": "treatment_mCherry_hND6_sample_number", + "id": "treatment_mCherry_hND6_sample_number_test", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "sample_number", "method": "deseq2" }, - "treatment_mCherry_hND6_sample_number_deseq2.deseq2.results.tsv:md5,2438053a4bdc869f467a12d3c22c7ba7" + "treatment_mCherry_hND6_sample_number_test_deseq2.deseq2.results.tsv:md5,2438053a4bdc869f467a12d3c22c7ba7" ] ], [ [ { - "id": "treatment_mCherry_hND6_", + "id": "treatment_mCherry_hND6__test", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -831,11 +831,11 @@ "fc_threshold": 1.5, "stat_threshold": 0.05 }, - "treatment_mCherry_hND6__filtered.tsv:md5,7829ead408f4c9cad4277598a231c494" + "treatment_mCherry_hND6__test_filtered.tsv:md5,7829ead408f4c9cad4277598a231c494" ], [ { - "id": "treatment_mCherry_hND6_sample_number", + "id": "treatment_mCherry_hND6_sample_number_test", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -844,7 +844,7 @@ "fc_threshold": 1.5, "stat_threshold": 0.05 }, - "treatment_mCherry_hND6_sample_number_filtered.tsv:md5,8b084475c9e7e1b34a510a73b613ff39" + "treatment_mCherry_hND6_sample_number_test_filtered.tsv:md5,8b084475c9e7e1b34a510a73b613ff39" ] ], [ @@ -870,25 +870,25 @@ [ [ { - "id": "treatment_mCherry_hND6_", + "id": "treatment_mCherry_hND6__test", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "", "method": "deseq2" }, - "treatment_mCherry_hND6__deseq2.deseq2.model.txt:md5,d2113d82b76046c319e6602da2ad74d6" + "treatment_mCherry_hND6__test_deseq2.deseq2.model.txt:md5,d2113d82b76046c319e6602da2ad74d6" ], [ { - "id": "treatment_mCherry_hND6_sample_number", + "id": "treatment_mCherry_hND6_sample_number_test", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "sample_number", "method": "deseq2" }, - "treatment_mCherry_hND6_sample_number_deseq2.deseq2.model.txt:md5,fa05126a58cb67c107d45426b0bdea83" + "treatment_mCherry_hND6_sample_number_test_deseq2.deseq2.model.txt:md5,fa05126a58cb67c107d45426b0bdea83" ] ], [ @@ -900,38 +900,38 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-01-31T13:49:54.987152774" + "timestamp": "2025-02-04T13:53:33.612999183" }, "deseq2 - with transcript lengths": { "content": [ [ [ { - "id": "treatment_mCherry_hND6_", + "id": "treatment_mCherry_hND6__test", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "", "method": "deseq2" }, - "treatment_mCherry_hND6__deseq2.deseq2.results.tsv:md5,944176b73455aa7c8de3ec32c03edef6" + "treatment_mCherry_hND6__test_deseq2.deseq2.results.tsv:md5,944176b73455aa7c8de3ec32c03edef6" ], [ { - "id": "treatment_mCherry_hND6_sample_number", + "id": "treatment_mCherry_hND6_sample_number_test", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "sample_number", "method": "deseq2" }, - "treatment_mCherry_hND6_sample_number_deseq2.deseq2.results.tsv:md5,6a9bc76c9d54034c90fa159372f97516" + "treatment_mCherry_hND6_sample_number_test_deseq2.deseq2.results.tsv:md5,6a9bc76c9d54034c90fa159372f97516" ] ], [ [ { - "id": "treatment_mCherry_hND6_", + "id": "treatment_mCherry_hND6__test", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -940,11 +940,11 @@ "fc_threshold": 1.5, "stat_threshold": 0.05 }, - "treatment_mCherry_hND6__filtered.tsv:md5,a48241fb5f24d961d3cce208f060b624" + "treatment_mCherry_hND6__test_filtered.tsv:md5,a48241fb5f24d961d3cce208f060b624" ], [ { - "id": "treatment_mCherry_hND6_sample_number", + "id": "treatment_mCherry_hND6_sample_number_test", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -953,7 +953,7 @@ "fc_threshold": 1.5, "stat_threshold": 0.05 }, - "treatment_mCherry_hND6_sample_number_filtered.tsv:md5,04d6911dce789f284c929694aa3d99b0" + "treatment_mCherry_hND6_sample_number_test_filtered.tsv:md5,04d6911dce789f284c929694aa3d99b0" ] ], [ @@ -979,25 +979,25 @@ [ [ { - "id": "treatment_mCherry_hND6_", + "id": "treatment_mCherry_hND6__test", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "", "method": "deseq2" }, - "treatment_mCherry_hND6__deseq2.deseq2.model.txt:md5,d2113d82b76046c319e6602da2ad74d6" + "treatment_mCherry_hND6__test_deseq2.deseq2.model.txt:md5,d2113d82b76046c319e6602da2ad74d6" ], [ { - "id": "treatment_mCherry_hND6_sample_number", + "id": "treatment_mCherry_hND6_sample_number_test", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "sample_number", "method": "deseq2" }, - "treatment_mCherry_hND6_sample_number_deseq2.deseq2.model.txt:md5,fa05126a58cb67c107d45426b0bdea83" + "treatment_mCherry_hND6_sample_number_test_deseq2.deseq2.model.txt:md5,fa05126a58cb67c107d45426b0bdea83" ] ], [ @@ -1009,38 +1009,38 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-01-31T13:52:00.181604697" + "timestamp": "2025-02-04T13:55:36.036520174" }, "propd - mouse - basic": { "content": [ [ [ { - "id": "treatment_mCherry_hND6_", + "id": "treatment_mCherry_hND6__test", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "", "method": "propd" }, - "treatment_mCherry_hND6_.propd.genewise.tsv:md5,bdc19a4b7430f248cd332287b630c872" + "treatment_mCherry_hND6__test.propd.genewise.tsv:md5,bdc19a4b7430f248cd332287b630c872" ], [ { - "id": "treatment_mCherry_hND6_sample_number", + "id": "treatment_mCherry_hND6_sample_number_test", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "sample_number", "method": "propd" }, - "treatment_mCherry_hND6_sample_number.propd.genewise.tsv:md5,bdc19a4b7430f248cd332287b630c872" + "treatment_mCherry_hND6_sample_number_test.propd.genewise.tsv:md5,bdc19a4b7430f248cd332287b630c872" ] ], [ [ { - "id": "treatment_mCherry_hND6_", + "id": "treatment_mCherry_hND6__test", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -1049,11 +1049,11 @@ "fc_threshold": 1.5, "stat_threshold": 100 }, - "treatment_mCherry_hND6__filtered.tsv:md5,432b2ba4e63fd8f7e2aee74e5b71b0a5" + "treatment_mCherry_hND6__test_filtered.tsv:md5,432b2ba4e63fd8f7e2aee74e5b71b0a5" ], [ { - "id": "treatment_mCherry_hND6_sample_number", + "id": "treatment_mCherry_hND6_sample_number_test", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -1062,31 +1062,31 @@ "fc_threshold": 1.5, "stat_threshold": 100 }, - "treatment_mCherry_hND6_sample_number_filtered.tsv:md5,432b2ba4e63fd8f7e2aee74e5b71b0a5" + "treatment_mCherry_hND6_sample_number_test_filtered.tsv:md5,432b2ba4e63fd8f7e2aee74e5b71b0a5" ] ], [ [ { - "id": "treatment_mCherry_hND6_", + "id": "treatment_mCherry_hND6__test", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "", "method": "propd" }, - "treatment_mCherry_hND6_.propd.adjacency.csv:md5,3a947ffd8172990c6207aa7561a41cb8" + "treatment_mCherry_hND6__test.propd.adjacency.csv:md5,3a947ffd8172990c6207aa7561a41cb8" ], [ { - "id": "treatment_mCherry_hND6_sample_number", + "id": "treatment_mCherry_hND6_sample_number_test", "variable": "treatment", "reference": "mCherry", "target": "hND6", "blocking": "sample_number", "method": "propd" }, - "treatment_mCherry_hND6_sample_number.propd.adjacency.csv:md5,3a947ffd8172990c6207aa7561a41cb8" + "treatment_mCherry_hND6_sample_number_test.propd.adjacency.csv:md5,3a947ffd8172990c6207aa7561a41cb8" ] ], [ @@ -1098,6 +1098,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-01-31T13:52:39.024496481" + "timestamp": "2025-02-04T13:55:58.53500005" } -} +} \ No newline at end of file diff --git a/subworkflows/nf-core/differential_functional_enrichment/main.nf b/subworkflows/nf-core/differential_functional_enrichment/main.nf index a2e3d0cc5ba..ff18aedc0f6 100644 --- a/subworkflows/nf-core/differential_functional_enrichment/main.nf +++ b/subworkflows/nf-core/differential_functional_enrichment/main.nf @@ -9,6 +9,12 @@ include { CUSTOM_TABULARTOGSEACHIP } from '../../../modules/nf-core/custom/tabul include { GSEA_GSEA } from '../../../modules/nf-core/gsea/gsea/main.nf' include { PROPR_GREA } from "../../../modules/nf-core/propr/grea/main.nf" +// Combine meta maps, including merging non-identical values of shared keys (e.g. 'id') +def mergeMaps(meta, meta2){ + (meta + meta2).collectEntries { k, v -> + meta[k] && meta[k] != v ? [k, "${meta[k]}_${v}"] : [k, v] + } +} workflow DIFFERENTIAL_FUNCTIONAL_ENRICHMENT { take: @@ -49,7 +55,7 @@ workflow DIFFERENTIAL_FUNCTIONAL_ENRICHMENT { def criteria = multiMapCriteria { meta_input, input, genesets, meta_exp, samplesheet, featuresheet, features_id, features_symbol, meta_contrasts, variable, reference, target -> def meta_contrasts_new = meta_contrasts + [ 'variable': variable, 'reference': reference, 'target': target ] // make sure variable, reference, target are in the meta - def meta_all = meta_input + meta_contrasts_new + def meta_all = mergeMaps(meta_contrasts_new, meta_input) input: [ meta_all, input ] genesets: diff --git a/subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test.snap b/subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test.snap index 9fd49d0fa47..696cf74cc91 100644 --- a/subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test.snap +++ b/subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test.snap @@ -4,7 +4,7 @@ [ [ { - "id": "treatment_mCherry_hND6_", + "id": "treatment_mCherry_hND6__test", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -14,11 +14,11 @@ "method_de": "deseq2", "method": "gprofiler2" }, - "treatment_mCherry_hND6_.gprofiler2.all_enriched_pathways.tsv:md5,10f7cef4ef0e1b0eab79818fdbaab9ad" + "treatment_mCherry_hND6__test.gprofiler2.all_enriched_pathways.tsv:md5,088003a4cbb5b6294f1c3efd7768ea6a" ], [ { - "id": "treatment_mCherry_hND6_", + "id": "treatment_mCherry_hND6__test", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -28,11 +28,11 @@ "method_de": "limma", "method": "gprofiler2" }, - "treatment_mCherry_hND6_.gprofiler2.all_enriched_pathways.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + "treatment_mCherry_hND6__test.gprofiler2.all_enriched_pathways.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ], [ { - "id": "treatment_mCherry_hND6_", + "id": "treatment_mCherry_hND6__test", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -42,11 +42,11 @@ "method_de": "propd", "method": "gprofiler2" }, - "treatment_mCherry_hND6_.gprofiler2.all_enriched_pathways.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + "treatment_mCherry_hND6__test.gprofiler2.all_enriched_pathways.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ], [ { - "id": "treatment_mCherry_hND6_sample_number", + "id": "treatment_mCherry_hND6_sample_number_test", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -56,11 +56,11 @@ "method_de": "deseq2", "method": "gprofiler2" }, - "treatment_mCherry_hND6_sample_number.gprofiler2.all_enriched_pathways.tsv:md5,7ac2c2f5c0ad3d72769419f065cb6ace" + "treatment_mCherry_hND6_sample_number_test.gprofiler2.all_enriched_pathways.tsv:md5,cd972792880248e9ad31be3fd2851a29" ], [ { - "id": "treatment_mCherry_hND6_sample_number", + "id": "treatment_mCherry_hND6_sample_number_test", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -70,11 +70,11 @@ "method_de": "limma", "method": "gprofiler2" }, - "treatment_mCherry_hND6_sample_number.gprofiler2.all_enriched_pathways.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + "treatment_mCherry_hND6_sample_number_test.gprofiler2.all_enriched_pathways.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ], [ { - "id": "treatment_mCherry_hND6_sample_number", + "id": "treatment_mCherry_hND6_sample_number_test", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -84,13 +84,13 @@ "method_de": "propd", "method": "gprofiler2" }, - "treatment_mCherry_hND6_sample_number.gprofiler2.all_enriched_pathways.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + "treatment_mCherry_hND6_sample_number_test.gprofiler2.all_enriched_pathways.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], [ [ { - "id": "treatment_mCherry_hND6_", + "id": "treatment_mCherry_hND6__test", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -101,15 +101,15 @@ "method": "gprofiler2" }, [ - "treatment_mCherry_hND6_.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,6047ffd74fe8a49db9b924485a441948", - "treatment_mCherry_hND6_.gprofiler2.GO:CC.sub_enriched_pathways.tsv:md5,891018299a66d62fbe979a56e9f31035", - "treatment_mCherry_hND6_.gprofiler2.GO:MF.sub_enriched_pathways.tsv:md5,46bb279062af777060495d56ac9767d7", - "treatment_mCherry_hND6_.gprofiler2.REAC.sub_enriched_pathways.tsv:md5,ca5e92673eb17242477e9c2787d68323" + "treatment_mCherry_hND6__test.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,6047ffd74fe8a49db9b924485a441948", + "treatment_mCherry_hND6__test.gprofiler2.GO:CC.sub_enriched_pathways.tsv:md5,891018299a66d62fbe979a56e9f31035", + "treatment_mCherry_hND6__test.gprofiler2.GO:MF.sub_enriched_pathways.tsv:md5,46bb279062af777060495d56ac9767d7", + "treatment_mCherry_hND6__test.gprofiler2.REAC.sub_enriched_pathways.tsv:md5,ca5e92673eb17242477e9c2787d68323" ] ], [ { - "id": "treatment_mCherry_hND6_sample_number", + "id": "treatment_mCherry_hND6_sample_number_test", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -120,75 +120,76 @@ "method": "gprofiler2" }, [ - "treatment_mCherry_hND6_sample_number.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,f55e010f72ee9200624137f42e94a5e5", - "treatment_mCherry_hND6_sample_number.gprofiler2.GO:CC.sub_enriched_pathways.tsv:md5,5bb51d9184e7257ce6cdd0ce7db16923", - "treatment_mCherry_hND6_sample_number.gprofiler2.GO:MF.sub_enriched_pathways.tsv:md5,210e4b99919354c79b37e12c83fdeaa5", - "treatment_mCherry_hND6_sample_number.gprofiler2.REAC.sub_enriched_pathways.tsv:md5,d754c55c2a2a1b8acda1c663165b4d2b" + "treatment_mCherry_hND6_sample_number_test.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,f55e010f72ee9200624137f42e94a5e5", + "treatment_mCherry_hND6_sample_number_test.gprofiler2.GO:CC.sub_enriched_pathways.tsv:md5,5bb51d9184e7257ce6cdd0ce7db16923", + "treatment_mCherry_hND6_sample_number_test.gprofiler2.GO:MF.sub_enriched_pathways.tsv:md5,210e4b99919354c79b37e12c83fdeaa5", + "treatment_mCherry_hND6_sample_number_test.gprofiler2.KEGG.sub_enriched_pathways.tsv:md5,3cbdbbb1c5b232ab73d35d4a0953d19c", + "treatment_mCherry_hND6_sample_number_test.gprofiler2.REAC.sub_enriched_pathways.tsv:md5,d754c55c2a2a1b8acda1c663165b4d2b" ] ] ], [ - "treatment_mCherry_hND6_.gprofiler2.gostplot.html", - "treatment_mCherry_hND6_sample_number.gprofiler2.gostplot.html" + "treatment_mCherry_hND6__test.gprofiler2.gostplot.html", + "treatment_mCherry_hND6_sample_number_test.gprofiler2.gostplot.html" ], [ [ { - "id": "treatment_mCherry_hND6_", - "method_de": "deseq2", - "method": "gsea", + "id": "treatment_mCherry_hND6__test", "variable": "treatment", "reference": "mCherry", "target": "hND6", - "blocking": "" + "blocking": "", + "method_de": "deseq2", + "method": "gsea" }, - "treatment_mCherry_hND6_.mh.all.v2022.1.Mm.symbols.gsea_report_for_mCherry.tsv:md5,ce8792382ae299749445767ff16aaecc", - "treatment_mCherry_hND6_.mh.all.v2022.1.Mm.symbols.gsea_report_for_hND6.tsv:md5,354a961c7e1417db2bf1f7e8d00c54f0" + "treatment_mCherry_hND6__test.mh.all.v2022.1.Mm.symbols.gsea_report_for_mCherry.tsv:md5,ce8792382ae299749445767ff16aaecc", + "treatment_mCherry_hND6__test.mh.all.v2022.1.Mm.symbols.gsea_report_for_hND6.tsv:md5,354a961c7e1417db2bf1f7e8d00c54f0" ], [ { - "id": "treatment_mCherry_hND6_", - "method_de": "limma", - "method": "gsea", + "id": "treatment_mCherry_hND6__test", "variable": "treatment", "reference": "mCherry", "target": "hND6", - "blocking": "" + "blocking": "", + "method_de": "limma", + "method": "gsea" }, - "treatment_mCherry_hND6_.mh.all.v2022.1.Mm.symbols.gsea_report_for_mCherry.tsv:md5,ce8792382ae299749445767ff16aaecc", - "treatment_mCherry_hND6_.mh.all.v2022.1.Mm.symbols.gsea_report_for_hND6.tsv:md5,a4dcc9581c9c63d35ef32ee0df882074" + "treatment_mCherry_hND6__test.mh.all.v2022.1.Mm.symbols.gsea_report_for_mCherry.tsv:md5,ce8792382ae299749445767ff16aaecc", + "treatment_mCherry_hND6__test.mh.all.v2022.1.Mm.symbols.gsea_report_for_hND6.tsv:md5,a4dcc9581c9c63d35ef32ee0df882074" ], [ { - "id": "treatment_mCherry_hND6_sample_number", - "method_de": "deseq2", - "method": "gsea", + "id": "treatment_mCherry_hND6_sample_number_test", "variable": "treatment", "reference": "mCherry", "target": "hND6", - "blocking": "sample_number" + "blocking": "sample_number", + "method_de": "deseq2", + "method": "gsea" }, - "treatment_mCherry_hND6_sample_number.mh.all.v2022.1.Mm.symbols.gsea_report_for_mCherry.tsv:md5,ce8792382ae299749445767ff16aaecc", - "treatment_mCherry_hND6_sample_number.mh.all.v2022.1.Mm.symbols.gsea_report_for_hND6.tsv:md5,354a961c7e1417db2bf1f7e8d00c54f0" + "treatment_mCherry_hND6_sample_number_test.mh.all.v2022.1.Mm.symbols.gsea_report_for_mCherry.tsv:md5,ce8792382ae299749445767ff16aaecc", + "treatment_mCherry_hND6_sample_number_test.mh.all.v2022.1.Mm.symbols.gsea_report_for_hND6.tsv:md5,354a961c7e1417db2bf1f7e8d00c54f0" ], [ { - "id": "treatment_mCherry_hND6_sample_number", - "method_de": "limma", - "method": "gsea", + "id": "treatment_mCherry_hND6_sample_number_test", "variable": "treatment", "reference": "mCherry", "target": "hND6", - "blocking": "sample_number" + "blocking": "sample_number", + "method_de": "limma", + "method": "gsea" }, - "treatment_mCherry_hND6_sample_number.mh.all.v2022.1.Mm.symbols.gsea_report_for_mCherry.tsv:md5,ce8792382ae299749445767ff16aaecc", - "treatment_mCherry_hND6_sample_number.mh.all.v2022.1.Mm.symbols.gsea_report_for_hND6.tsv:md5,a4dcc9581c9c63d35ef32ee0df882074" + "treatment_mCherry_hND6_sample_number_test.mh.all.v2022.1.Mm.symbols.gsea_report_for_mCherry.tsv:md5,ce8792382ae299749445767ff16aaecc", + "treatment_mCherry_hND6_sample_number_test.mh.all.v2022.1.Mm.symbols.gsea_report_for_hND6.tsv:md5,a4dcc9581c9c63d35ef32ee0df882074" ] ], [ [ { - "id": "treatment_mCherry_hND6_", + "id": "treatment_mCherry_hND6__test", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -196,11 +197,11 @@ "method_de": "propd", "method": "grea" }, - "treatment_mCherry_hND6_.grea.tsv:md5,786faeccf39926d2f7c980ef549a2697" + "treatment_mCherry_hND6__test.grea.tsv:md5,786faeccf39926d2f7c980ef549a2697" ], [ { - "id": "treatment_mCherry_hND6_sample_number", + "id": "treatment_mCherry_hND6_sample_number_test", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -208,7 +209,7 @@ "method_de": "propd", "method": "grea" }, - "treatment_mCherry_hND6_sample_number.grea.tsv:md5,786faeccf39926d2f7c980ef549a2697" + "treatment_mCherry_hND6_sample_number_test.grea.tsv:md5,786faeccf39926d2f7c980ef549a2697" ] ], [ @@ -239,14 +240,14 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-01-31T14:38:55.322768786" + "timestamp": "2025-02-04T14:09:32.804178552" }, "propd + grea - mouse": { "content": [ [ [ { - "id": "treatment_mCherry_hND6_", + "id": "treatment_mCherry_hND6__test", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -254,11 +255,11 @@ "method_de": "propd", "method": "grea" }, - "treatment_mCherry_hND6_.grea.tsv:md5,786faeccf39926d2f7c980ef549a2697" + "treatment_mCherry_hND6__test.grea.tsv:md5,786faeccf39926d2f7c980ef549a2697" ], [ { - "id": "treatment_mCherry_hND6_sample_number", + "id": "treatment_mCherry_hND6_sample_number_test", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -266,7 +267,7 @@ "method_de": "propd", "method": "grea" }, - "treatment_mCherry_hND6_sample_number.grea.tsv:md5,786faeccf39926d2f7c980ef549a2697" + "treatment_mCherry_hND6_sample_number_test.grea.tsv:md5,786faeccf39926d2f7c980ef549a2697" ] ], { @@ -283,14 +284,14 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-01-31T14:35:38.838594087" + "timestamp": "2025-02-04T14:08:03.665178563" }, "deseq2 + gprofiler2 - mouse": { "content": [ [ [ { - "id": "treatment_mCherry_hND6_", + "id": "treatment_mCherry_hND6__test", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -300,11 +301,11 @@ "method_de": "deseq2", "method": "gprofiler2" }, - "treatment_mCherry_hND6_.gprofiler2.all_enriched_pathways.tsv:md5,10f7cef4ef0e1b0eab79818fdbaab9ad" + "treatment_mCherry_hND6__test.gprofiler2.all_enriched_pathways.tsv:md5,088003a4cbb5b6294f1c3efd7768ea6a" ], [ { - "id": "treatment_mCherry_hND6_sample_number", + "id": "treatment_mCherry_hND6_sample_number_test", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -314,13 +315,13 @@ "method_de": "deseq2", "method": "gprofiler2" }, - "treatment_mCherry_hND6_sample_number.gprofiler2.all_enriched_pathways.tsv:md5,7ac2c2f5c0ad3d72769419f065cb6ace" + "treatment_mCherry_hND6_sample_number_test.gprofiler2.all_enriched_pathways.tsv:md5,cd972792880248e9ad31be3fd2851a29" ] ], [ [ { - "id": "treatment_mCherry_hND6_", + "id": "treatment_mCherry_hND6__test", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -331,15 +332,15 @@ "method": "gprofiler2" }, [ - "treatment_mCherry_hND6_.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,6047ffd74fe8a49db9b924485a441948", - "treatment_mCherry_hND6_.gprofiler2.GO:CC.sub_enriched_pathways.tsv:md5,891018299a66d62fbe979a56e9f31035", - "treatment_mCherry_hND6_.gprofiler2.GO:MF.sub_enriched_pathways.tsv:md5,46bb279062af777060495d56ac9767d7", - "treatment_mCherry_hND6_.gprofiler2.REAC.sub_enriched_pathways.tsv:md5,ca5e92673eb17242477e9c2787d68323" + "treatment_mCherry_hND6__test.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,6047ffd74fe8a49db9b924485a441948", + "treatment_mCherry_hND6__test.gprofiler2.GO:CC.sub_enriched_pathways.tsv:md5,891018299a66d62fbe979a56e9f31035", + "treatment_mCherry_hND6__test.gprofiler2.GO:MF.sub_enriched_pathways.tsv:md5,46bb279062af777060495d56ac9767d7", + "treatment_mCherry_hND6__test.gprofiler2.REAC.sub_enriched_pathways.tsv:md5,ca5e92673eb17242477e9c2787d68323" ] ], [ { - "id": "treatment_mCherry_hND6_sample_number", + "id": "treatment_mCherry_hND6_sample_number_test", "variable": "treatment", "reference": "mCherry", "target": "hND6", @@ -350,16 +351,17 @@ "method": "gprofiler2" }, [ - "treatment_mCherry_hND6_sample_number.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,f55e010f72ee9200624137f42e94a5e5", - "treatment_mCherry_hND6_sample_number.gprofiler2.GO:CC.sub_enriched_pathways.tsv:md5,5bb51d9184e7257ce6cdd0ce7db16923", - "treatment_mCherry_hND6_sample_number.gprofiler2.GO:MF.sub_enriched_pathways.tsv:md5,210e4b99919354c79b37e12c83fdeaa5", - "treatment_mCherry_hND6_sample_number.gprofiler2.REAC.sub_enriched_pathways.tsv:md5,d754c55c2a2a1b8acda1c663165b4d2b" + "treatment_mCherry_hND6_sample_number_test.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,f55e010f72ee9200624137f42e94a5e5", + "treatment_mCherry_hND6_sample_number_test.gprofiler2.GO:CC.sub_enriched_pathways.tsv:md5,5bb51d9184e7257ce6cdd0ce7db16923", + "treatment_mCherry_hND6_sample_number_test.gprofiler2.GO:MF.sub_enriched_pathways.tsv:md5,210e4b99919354c79b37e12c83fdeaa5", + "treatment_mCherry_hND6_sample_number_test.gprofiler2.KEGG.sub_enriched_pathways.tsv:md5,3cbdbbb1c5b232ab73d35d4a0953d19c", + "treatment_mCherry_hND6_sample_number_test.gprofiler2.REAC.sub_enriched_pathways.tsv:md5,d754c55c2a2a1b8acda1c663165b4d2b" ] ] ], [ - "treatment_mCherry_hND6_.gprofiler2.gostplot.html", - "treatment_mCherry_hND6_sample_number.gprofiler2.gostplot.html" + "treatment_mCherry_hND6__test.gprofiler2.gostplot.html", + "treatment_mCherry_hND6_sample_number_test.gprofiler2.gostplot.html" ], { "DIFFERENTIAL_FUNCTIONAL_ENRICHMENT:GPROFILER2_GOST": { @@ -377,7 +379,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-01-31T14:32:57.471420763" + "timestamp": "2025-02-04T14:06:20.150561495" }, "test gprofiler2 - mouse": { "content": [ @@ -391,7 +393,7 @@ "blocking": "batch", "method": "gprofiler2" }, - "Condition_genotype_WT_KO.gprofiler2.all_enriched_pathways.tsv:md5,396712577c32213078d1604b1ba247de" + "Condition_genotype_WT_KO.gprofiler2.all_enriched_pathways.tsv:md5,31d1e4cfa1d09b30bf9126415cb93aff" ] ], [ @@ -405,13 +407,14 @@ "method": "gprofiler2" }, [ - "Condition_genotype_WT_KO.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,d6bebdcb2401a7f7de0ec42ad2f4521d", + "Condition_genotype_WT_KO.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,6211f4fa1a226f3aaab77c3fb9318fe7", "Condition_genotype_WT_KO.gprofiler2.GO:CC.sub_enriched_pathways.tsv:md5,98a49b69f8b724d88d6367dea494ca53", "Condition_genotype_WT_KO.gprofiler2.GO:MF.sub_enriched_pathways.tsv:md5,39ce8238319df47708df78b1c461a89d", "Condition_genotype_WT_KO.gprofiler2.HP.sub_enriched_pathways.tsv:md5,616f3a5d19844001bb8aac38049e987a", - "Condition_genotype_WT_KO.gprofiler2.MIRNA.sub_enriched_pathways.tsv:md5,486ed1510dc8bba867686b021d6e6339", + "Condition_genotype_WT_KO.gprofiler2.KEGG.sub_enriched_pathways.tsv:md5,413724002abe683f376ea914d4f21ade", + "Condition_genotype_WT_KO.gprofiler2.MIRNA.sub_enriched_pathways.tsv:md5,9168f1d7f7d1b1db18a4652db05b81b6", "Condition_genotype_WT_KO.gprofiler2.REAC.sub_enriched_pathways.tsv:md5,3571ac765c47e1c38c63c463465f2a1e", - "Condition_genotype_WT_KO.gprofiler2.TF.sub_enriched_pathways.tsv:md5,032491e63bb381cc9a4d7740473efc5b", + "Condition_genotype_WT_KO.gprofiler2.TF.sub_enriched_pathways.tsv:md5,4d23e5fdc96395ea79d174b1afe84756", "Condition_genotype_WT_KO.gprofiler2.WP.sub_enriched_pathways.tsv:md5,e99c42df912a9ee75c7197f92d615979" ] ] @@ -434,36 +437,36 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-01-31T14:31:40.671620493" + "timestamp": "2025-02-04T14:05:08.208687138" }, "deseq2 + gsea - mouse": { "content": [ [ [ { - "id": "treatment_mCherry_hND6_", - "method_de": "deseq2", - "method": "gsea", + "id": "treatment_mCherry_hND6__test", "variable": "treatment", "reference": "mCherry", "target": "hND6", - "blocking": "" + "blocking": "", + "method_de": "deseq2", + "method": "gsea" }, - "treatment_mCherry_hND6_.mh.all.v2022.1.Mm.symbols.gsea_report_for_mCherry.tsv:md5,ce8792382ae299749445767ff16aaecc", - "treatment_mCherry_hND6_.mh.all.v2022.1.Mm.symbols.gsea_report_for_hND6.tsv:md5,354a961c7e1417db2bf1f7e8d00c54f0" + "treatment_mCherry_hND6__test.mh.all.v2022.1.Mm.symbols.gsea_report_for_mCherry.tsv:md5,ce8792382ae299749445767ff16aaecc", + "treatment_mCherry_hND6__test.mh.all.v2022.1.Mm.symbols.gsea_report_for_hND6.tsv:md5,354a961c7e1417db2bf1f7e8d00c54f0" ], [ { - "id": "treatment_mCherry_hND6_sample_number", - "method_de": "deseq2", - "method": "gsea", + "id": "treatment_mCherry_hND6_sample_number_test", "variable": "treatment", "reference": "mCherry", "target": "hND6", - "blocking": "sample_number" + "blocking": "sample_number", + "method_de": "deseq2", + "method": "gsea" }, - "treatment_mCherry_hND6_sample_number.mh.all.v2022.1.Mm.symbols.gsea_report_for_mCherry.tsv:md5,ce8792382ae299749445767ff16aaecc", - "treatment_mCherry_hND6_sample_number.mh.all.v2022.1.Mm.symbols.gsea_report_for_hND6.tsv:md5,354a961c7e1417db2bf1f7e8d00c54f0" + "treatment_mCherry_hND6_sample_number_test.mh.all.v2022.1.Mm.symbols.gsea_report_for_mCherry.tsv:md5,ce8792382ae299749445767ff16aaecc", + "treatment_mCherry_hND6_sample_number_test.mh.all.v2022.1.Mm.symbols.gsea_report_for_hND6.tsv:md5,354a961c7e1417db2bf1f7e8d00c54f0" ] ], { @@ -485,7 +488,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-01-31T14:34:55.565980336" + "timestamp": "2025-02-04T14:07:37.044833142" }, "stub": { "content": [ @@ -530,10 +533,10 @@ ] ], "3": [ - + ], "4": [ - + ], "5": [ "versions.yml:md5,7861e3047b941b86ef50124168a13b51" @@ -578,10 +581,10 @@ ] ], "grea_results": [ - + ], "gsea_report": [ - + ], "versions": [ "versions.yml:md5,7861e3047b941b86ef50124168a13b51" @@ -594,4 +597,4 @@ }, "timestamp": "2025-01-24T17:38:14.74535" } -} \ No newline at end of file +} From e882d58de17c0728dac8edf29ccc46132ea21548 Mon Sep 17 00:00:00 2001 From: Suzanne Jin Date: Tue, 4 Feb 2025 15:31:28 +0000 Subject: [PATCH 09/15] fix(snapshot): update gprofiler2/gost test snapshots --- .../nf-core/gprofiler2/gost/tests/main.nf.test.snap | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/modules/nf-core/gprofiler2/gost/tests/main.nf.test.snap b/modules/nf-core/gprofiler2/gost/tests/main.nf.test.snap index 189aee66a03..957042bdb72 100644 --- a/modules/nf-core/gprofiler2/gost/tests/main.nf.test.snap +++ b/modules/nf-core/gprofiler2/gost/tests/main.nf.test.snap @@ -10,7 +10,7 @@ "target": "KO", "blocking": "batch" }, - "Condition_genotype_WT_KO.gprofiler2.all_enriched_pathways.tsv:md5,396712577c32213078d1604b1ba247de" + "Condition_genotype_WT_KO.gprofiler2.all_enriched_pathways.tsv:md5,31d1e4cfa1d09b30bf9126415cb93aff" ] ], [ @@ -23,13 +23,14 @@ "blocking": "batch" }, [ - "Condition_genotype_WT_KO.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,d6bebdcb2401a7f7de0ec42ad2f4521d", + "Condition_genotype_WT_KO.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,6211f4fa1a226f3aaab77c3fb9318fe7", "Condition_genotype_WT_KO.gprofiler2.GO:CC.sub_enriched_pathways.tsv:md5,98a49b69f8b724d88d6367dea494ca53", "Condition_genotype_WT_KO.gprofiler2.GO:MF.sub_enriched_pathways.tsv:md5,39ce8238319df47708df78b1c461a89d", "Condition_genotype_WT_KO.gprofiler2.HP.sub_enriched_pathways.tsv:md5,616f3a5d19844001bb8aac38049e987a", - "Condition_genotype_WT_KO.gprofiler2.MIRNA.sub_enriched_pathways.tsv:md5,486ed1510dc8bba867686b021d6e6339", + "Condition_genotype_WT_KO.gprofiler2.KEGG.sub_enriched_pathways.tsv:md5,413724002abe683f376ea914d4f21ade", + "Condition_genotype_WT_KO.gprofiler2.MIRNA.sub_enriched_pathways.tsv:md5,9168f1d7f7d1b1db18a4652db05b81b6", "Condition_genotype_WT_KO.gprofiler2.REAC.sub_enriched_pathways.tsv:md5,3571ac765c47e1c38c63c463465f2a1e", - "Condition_genotype_WT_KO.gprofiler2.TF.sub_enriched_pathways.tsv:md5,032491e63bb381cc9a4d7740473efc5b", + "Condition_genotype_WT_KO.gprofiler2.TF.sub_enriched_pathways.tsv:md5,4d23e5fdc96395ea79d174b1afe84756", "Condition_genotype_WT_KO.gprofiler2.WP.sub_enriched_pathways.tsv:md5,e99c42df912a9ee75c7197f92d615979" ] ] @@ -40,6 +41,7 @@ "Condition_genotype_WT_KO.gprofiler2.GO:CC.sub_enriched_pathways.png", "Condition_genotype_WT_KO.gprofiler2.GO:MF.sub_enriched_pathways.png", "Condition_genotype_WT_KO.gprofiler2.HP.sub_enriched_pathways.png", + "Condition_genotype_WT_KO.gprofiler2.KEGG.sub_enriched_pathways.png", "Condition_genotype_WT_KO.gprofiler2.MIRNA.sub_enriched_pathways.png", "Condition_genotype_WT_KO.gprofiler2.REAC.sub_enriched_pathways.png", "Condition_genotype_WT_KO.gprofiler2.TF.sub_enriched_pathways.png", @@ -65,7 +67,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-01-31T15:16:54.617930264" + "timestamp": "2025-02-04T15:17:47.835304298" }, "stub": { "content": [ From 0a0aee1e7869adafb52901242e393605511e8bea Mon Sep 17 00:00:00 2001 From: Suzanne Jin Date: Wed, 5 Feb 2025 11:06:24 +0000 Subject: [PATCH 10/15] fix(gprofiler2_gost): set base url to an old archive for reproducibility. --- .../gost/templates/gprofiler2_gost.R | 4 +- .../gprofiler2/gost/tests/main.nf.test.snap | 20 ++--- .../tests/all.config | 3 +- .../tests/deseq2_gprofiler2.config | 3 +- .../tests/gprofiler2.config | 3 +- .../tests/main.nf.test.snap | 74 +++++++++---------- 6 files changed, 56 insertions(+), 51 deletions(-) diff --git a/modules/nf-core/gprofiler2/gost/templates/gprofiler2_gost.R b/modules/nf-core/gprofiler2/gost/templates/gprofiler2_gost.R index ce50aa38d41..b8fba8d043a 100644 --- a/modules/nf-core/gprofiler2/gost/templates/gprofiler2_gost.R +++ b/modules/nf-core/gprofiler2/gost/templates/gprofiler2_gost.R @@ -236,7 +236,9 @@ if (nrow(de.genes) > 0) { } else if (!is.null(opt\$organism)) { # Next, check if organism was provided. Get the GMT file from gprofiler and save both the full file as well as the filtered one to metadata - gmt_url <- paste0("https://biit.cs.ut.ee/", opt\$archive, "//static/gprofiler_full_", opt\$organism, ".ENSG.gmt") + base_url <- paste0("https://biit.cs.ut.ee/", opt\$archive) + gmt_url <- paste0(base_url, "//static/gprofiler_full_", opt\$organism, ".ENSG.gmt") + set_base_url(base_url) tryCatch( { gmt_path <- paste0("gprofiler_full_", opt\$organism, ".ENSG.gmt") diff --git a/modules/nf-core/gprofiler2/gost/tests/main.nf.test.snap b/modules/nf-core/gprofiler2/gost/tests/main.nf.test.snap index 957042bdb72..9b8920030ff 100644 --- a/modules/nf-core/gprofiler2/gost/tests/main.nf.test.snap +++ b/modules/nf-core/gprofiler2/gost/tests/main.nf.test.snap @@ -10,7 +10,7 @@ "target": "KO", "blocking": "batch" }, - "Condition_genotype_WT_KO.gprofiler2.all_enriched_pathways.tsv:md5,31d1e4cfa1d09b30bf9126415cb93aff" + "Condition_genotype_WT_KO.gprofiler2.all_enriched_pathways.tsv:md5,1134a02ca061c463bcbff277eefbfb19" ] ], [ @@ -23,15 +23,15 @@ "blocking": "batch" }, [ - "Condition_genotype_WT_KO.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,6211f4fa1a226f3aaab77c3fb9318fe7", - "Condition_genotype_WT_KO.gprofiler2.GO:CC.sub_enriched_pathways.tsv:md5,98a49b69f8b724d88d6367dea494ca53", - "Condition_genotype_WT_KO.gprofiler2.GO:MF.sub_enriched_pathways.tsv:md5,39ce8238319df47708df78b1c461a89d", - "Condition_genotype_WT_KO.gprofiler2.HP.sub_enriched_pathways.tsv:md5,616f3a5d19844001bb8aac38049e987a", + "Condition_genotype_WT_KO.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,d527b94cdb160070bcaa0bfb0cecf914", + "Condition_genotype_WT_KO.gprofiler2.GO:CC.sub_enriched_pathways.tsv:md5,ef418c3f06d50446317928e37ec8ddfb", + "Condition_genotype_WT_KO.gprofiler2.GO:MF.sub_enriched_pathways.tsv:md5,e460d4917feb0b64d334a528f59e0731", + "Condition_genotype_WT_KO.gprofiler2.HP.sub_enriched_pathways.tsv:md5,865d8f092503552831c51d775a98c6eb", "Condition_genotype_WT_KO.gprofiler2.KEGG.sub_enriched_pathways.tsv:md5,413724002abe683f376ea914d4f21ade", - "Condition_genotype_WT_KO.gprofiler2.MIRNA.sub_enriched_pathways.tsv:md5,9168f1d7f7d1b1db18a4652db05b81b6", - "Condition_genotype_WT_KO.gprofiler2.REAC.sub_enriched_pathways.tsv:md5,3571ac765c47e1c38c63c463465f2a1e", - "Condition_genotype_WT_KO.gprofiler2.TF.sub_enriched_pathways.tsv:md5,4d23e5fdc96395ea79d174b1afe84756", - "Condition_genotype_WT_KO.gprofiler2.WP.sub_enriched_pathways.tsv:md5,e99c42df912a9ee75c7197f92d615979" + "Condition_genotype_WT_KO.gprofiler2.MIRNA.sub_enriched_pathways.tsv:md5,fce81051d7af955ddb2925ba2da9ff57", + "Condition_genotype_WT_KO.gprofiler2.REAC.sub_enriched_pathways.tsv:md5,e89e1876698ea644671a0720c85f4dbb", + "Condition_genotype_WT_KO.gprofiler2.TF.sub_enriched_pathways.tsv:md5,e272217ec7fcf01ea463ab8bcc8335cf", + "Condition_genotype_WT_KO.gprofiler2.WP.sub_enriched_pathways.tsv:md5,fdd1efa836d85bb127e933e925290cba" ] ] ], @@ -67,7 +67,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-04T15:17:47.835304298" + "timestamp": "2025-02-05T10:35:35.015326132" }, "stub": { "content": [ diff --git a/subworkflows/nf-core/differential_functional_enrichment/tests/all.config b/subworkflows/nf-core/differential_functional_enrichment/tests/all.config index 7f092f0d879..79618c1c100 100644 --- a/subworkflows/nf-core/differential_functional_enrichment/tests/all.config +++ b/subworkflows/nf-core/differential_functional_enrichment/tests/all.config @@ -45,7 +45,8 @@ process { "--round_digits 4", "--palette_name Blues", "--de_id_column gene_id", - "--organism mmusculus" + "--organism mmusculus", + "--archive gprofiler_archive3/e111_eg58_p18" ].join(' ').trim() } diff --git a/subworkflows/nf-core/differential_functional_enrichment/tests/deseq2_gprofiler2.config b/subworkflows/nf-core/differential_functional_enrichment/tests/deseq2_gprofiler2.config index 458bb6dda14..3816b40cfcf 100644 --- a/subworkflows/nf-core/differential_functional_enrichment/tests/deseq2_gprofiler2.config +++ b/subworkflows/nf-core/differential_functional_enrichment/tests/deseq2_gprofiler2.config @@ -24,7 +24,8 @@ process { "--round_digits 4", "--palette_name Blues", "--de_id_column gene_id", - "--organism mmusculus" + "--organism mmusculus", + "--archive gprofiler_archive3/e111_eg58_p18" ].join(' ').trim() } } diff --git a/subworkflows/nf-core/differential_functional_enrichment/tests/gprofiler2.config b/subworkflows/nf-core/differential_functional_enrichment/tests/gprofiler2.config index 1fe3a1c9b48..05e24571543 100644 --- a/subworkflows/nf-core/differential_functional_enrichment/tests/gprofiler2.config +++ b/subworkflows/nf-core/differential_functional_enrichment/tests/gprofiler2.config @@ -11,7 +11,8 @@ process { "--round_digits 4", "--palette_name Blues", "--de_id_column gene_id", - "--organism mmusculus" + "--organism mmusculus", + "--archive gprofiler_archive3/e111_eg58_p18" ].join(' ').trim() } } diff --git a/subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test.snap b/subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test.snap index 696cf74cc91..776f57fd6d7 100644 --- a/subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test.snap +++ b/subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "method_de": "deseq2", "method": "gprofiler2" }, - "treatment_mCherry_hND6__test.gprofiler2.all_enriched_pathways.tsv:md5,088003a4cbb5b6294f1c3efd7768ea6a" + "treatment_mCherry_hND6__test.gprofiler2.all_enriched_pathways.tsv:md5,d586d92fb6cc3e41d493d14c4d9a7d92" ], [ { @@ -56,7 +56,7 @@ "method_de": "deseq2", "method": "gprofiler2" }, - "treatment_mCherry_hND6_sample_number_test.gprofiler2.all_enriched_pathways.tsv:md5,cd972792880248e9ad31be3fd2851a29" + "treatment_mCherry_hND6_sample_number_test.gprofiler2.all_enriched_pathways.tsv:md5,fa880c70d06f56d8dad0ac8078e6233c" ], [ { @@ -101,10 +101,10 @@ "method": "gprofiler2" }, [ - "treatment_mCherry_hND6__test.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,6047ffd74fe8a49db9b924485a441948", - "treatment_mCherry_hND6__test.gprofiler2.GO:CC.sub_enriched_pathways.tsv:md5,891018299a66d62fbe979a56e9f31035", - "treatment_mCherry_hND6__test.gprofiler2.GO:MF.sub_enriched_pathways.tsv:md5,46bb279062af777060495d56ac9767d7", - "treatment_mCherry_hND6__test.gprofiler2.REAC.sub_enriched_pathways.tsv:md5,ca5e92673eb17242477e9c2787d68323" + "treatment_mCherry_hND6__test.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,4c95059438af872253aa95a5ff127fca", + "treatment_mCherry_hND6__test.gprofiler2.GO:CC.sub_enriched_pathways.tsv:md5,b4e4009e067f723694efc1a46a609e2b", + "treatment_mCherry_hND6__test.gprofiler2.GO:MF.sub_enriched_pathways.tsv:md5,ece72606ce6d1d037cfd5f5b198233a8", + "treatment_mCherry_hND6__test.gprofiler2.REAC.sub_enriched_pathways.tsv:md5,dc7b6f67903e25076ab95a7e1bb39bbe" ] ], [ @@ -120,11 +120,11 @@ "method": "gprofiler2" }, [ - "treatment_mCherry_hND6_sample_number_test.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,f55e010f72ee9200624137f42e94a5e5", - "treatment_mCherry_hND6_sample_number_test.gprofiler2.GO:CC.sub_enriched_pathways.tsv:md5,5bb51d9184e7257ce6cdd0ce7db16923", - "treatment_mCherry_hND6_sample_number_test.gprofiler2.GO:MF.sub_enriched_pathways.tsv:md5,210e4b99919354c79b37e12c83fdeaa5", + "treatment_mCherry_hND6_sample_number_test.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,dc27af1c941636f8b03e8c8724773725", + "treatment_mCherry_hND6_sample_number_test.gprofiler2.GO:CC.sub_enriched_pathways.tsv:md5,09b7770d59d2efa8a58f300a16a41ae7", + "treatment_mCherry_hND6_sample_number_test.gprofiler2.GO:MF.sub_enriched_pathways.tsv:md5,a261d658ca1b1ec0511e55da734d7810", "treatment_mCherry_hND6_sample_number_test.gprofiler2.KEGG.sub_enriched_pathways.tsv:md5,3cbdbbb1c5b232ab73d35d4a0953d19c", - "treatment_mCherry_hND6_sample_number_test.gprofiler2.REAC.sub_enriched_pathways.tsv:md5,d754c55c2a2a1b8acda1c663165b4d2b" + "treatment_mCherry_hND6_sample_number_test.gprofiler2.REAC.sub_enriched_pathways.tsv:md5,8472cb5792bf7ec044bb95df356ad47e" ] ] ], @@ -240,7 +240,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-04T14:09:32.804178552" + "timestamp": "2025-02-05T11:01:43.994943675" }, "propd + grea - mouse": { "content": [ @@ -301,7 +301,7 @@ "method_de": "deseq2", "method": "gprofiler2" }, - "treatment_mCherry_hND6__test.gprofiler2.all_enriched_pathways.tsv:md5,088003a4cbb5b6294f1c3efd7768ea6a" + "treatment_mCherry_hND6__test.gprofiler2.all_enriched_pathways.tsv:md5,d586d92fb6cc3e41d493d14c4d9a7d92" ], [ { @@ -315,7 +315,7 @@ "method_de": "deseq2", "method": "gprofiler2" }, - "treatment_mCherry_hND6_sample_number_test.gprofiler2.all_enriched_pathways.tsv:md5,cd972792880248e9ad31be3fd2851a29" + "treatment_mCherry_hND6_sample_number_test.gprofiler2.all_enriched_pathways.tsv:md5,fa880c70d06f56d8dad0ac8078e6233c" ] ], [ @@ -332,10 +332,10 @@ "method": "gprofiler2" }, [ - "treatment_mCherry_hND6__test.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,6047ffd74fe8a49db9b924485a441948", - "treatment_mCherry_hND6__test.gprofiler2.GO:CC.sub_enriched_pathways.tsv:md5,891018299a66d62fbe979a56e9f31035", - "treatment_mCherry_hND6__test.gprofiler2.GO:MF.sub_enriched_pathways.tsv:md5,46bb279062af777060495d56ac9767d7", - "treatment_mCherry_hND6__test.gprofiler2.REAC.sub_enriched_pathways.tsv:md5,ca5e92673eb17242477e9c2787d68323" + "treatment_mCherry_hND6__test.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,4c95059438af872253aa95a5ff127fca", + "treatment_mCherry_hND6__test.gprofiler2.GO:CC.sub_enriched_pathways.tsv:md5,b4e4009e067f723694efc1a46a609e2b", + "treatment_mCherry_hND6__test.gprofiler2.GO:MF.sub_enriched_pathways.tsv:md5,ece72606ce6d1d037cfd5f5b198233a8", + "treatment_mCherry_hND6__test.gprofiler2.REAC.sub_enriched_pathways.tsv:md5,dc7b6f67903e25076ab95a7e1bb39bbe" ] ], [ @@ -351,11 +351,11 @@ "method": "gprofiler2" }, [ - "treatment_mCherry_hND6_sample_number_test.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,f55e010f72ee9200624137f42e94a5e5", - "treatment_mCherry_hND6_sample_number_test.gprofiler2.GO:CC.sub_enriched_pathways.tsv:md5,5bb51d9184e7257ce6cdd0ce7db16923", - "treatment_mCherry_hND6_sample_number_test.gprofiler2.GO:MF.sub_enriched_pathways.tsv:md5,210e4b99919354c79b37e12c83fdeaa5", + "treatment_mCherry_hND6_sample_number_test.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,dc27af1c941636f8b03e8c8724773725", + "treatment_mCherry_hND6_sample_number_test.gprofiler2.GO:CC.sub_enriched_pathways.tsv:md5,09b7770d59d2efa8a58f300a16a41ae7", + "treatment_mCherry_hND6_sample_number_test.gprofiler2.GO:MF.sub_enriched_pathways.tsv:md5,a261d658ca1b1ec0511e55da734d7810", "treatment_mCherry_hND6_sample_number_test.gprofiler2.KEGG.sub_enriched_pathways.tsv:md5,3cbdbbb1c5b232ab73d35d4a0953d19c", - "treatment_mCherry_hND6_sample_number_test.gprofiler2.REAC.sub_enriched_pathways.tsv:md5,d754c55c2a2a1b8acda1c663165b4d2b" + "treatment_mCherry_hND6_sample_number_test.gprofiler2.REAC.sub_enriched_pathways.tsv:md5,8472cb5792bf7ec044bb95df356ad47e" ] ] ], @@ -379,7 +379,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-04T14:06:20.150561495" + "timestamp": "2025-02-05T10:50:42.142874287" }, "test gprofiler2 - mouse": { "content": [ @@ -393,7 +393,7 @@ "blocking": "batch", "method": "gprofiler2" }, - "Condition_genotype_WT_KO.gprofiler2.all_enriched_pathways.tsv:md5,31d1e4cfa1d09b30bf9126415cb93aff" + "Condition_genotype_WT_KO.gprofiler2.all_enriched_pathways.tsv:md5,1134a02ca061c463bcbff277eefbfb19" ] ], [ @@ -407,15 +407,15 @@ "method": "gprofiler2" }, [ - "Condition_genotype_WT_KO.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,6211f4fa1a226f3aaab77c3fb9318fe7", - "Condition_genotype_WT_KO.gprofiler2.GO:CC.sub_enriched_pathways.tsv:md5,98a49b69f8b724d88d6367dea494ca53", - "Condition_genotype_WT_KO.gprofiler2.GO:MF.sub_enriched_pathways.tsv:md5,39ce8238319df47708df78b1c461a89d", - "Condition_genotype_WT_KO.gprofiler2.HP.sub_enriched_pathways.tsv:md5,616f3a5d19844001bb8aac38049e987a", + "Condition_genotype_WT_KO.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,d527b94cdb160070bcaa0bfb0cecf914", + "Condition_genotype_WT_KO.gprofiler2.GO:CC.sub_enriched_pathways.tsv:md5,ef418c3f06d50446317928e37ec8ddfb", + "Condition_genotype_WT_KO.gprofiler2.GO:MF.sub_enriched_pathways.tsv:md5,e460d4917feb0b64d334a528f59e0731", + "Condition_genotype_WT_KO.gprofiler2.HP.sub_enriched_pathways.tsv:md5,865d8f092503552831c51d775a98c6eb", "Condition_genotype_WT_KO.gprofiler2.KEGG.sub_enriched_pathways.tsv:md5,413724002abe683f376ea914d4f21ade", - "Condition_genotype_WT_KO.gprofiler2.MIRNA.sub_enriched_pathways.tsv:md5,9168f1d7f7d1b1db18a4652db05b81b6", - "Condition_genotype_WT_KO.gprofiler2.REAC.sub_enriched_pathways.tsv:md5,3571ac765c47e1c38c63c463465f2a1e", - "Condition_genotype_WT_KO.gprofiler2.TF.sub_enriched_pathways.tsv:md5,4d23e5fdc96395ea79d174b1afe84756", - "Condition_genotype_WT_KO.gprofiler2.WP.sub_enriched_pathways.tsv:md5,e99c42df912a9ee75c7197f92d615979" + "Condition_genotype_WT_KO.gprofiler2.MIRNA.sub_enriched_pathways.tsv:md5,fce81051d7af955ddb2925ba2da9ff57", + "Condition_genotype_WT_KO.gprofiler2.REAC.sub_enriched_pathways.tsv:md5,e89e1876698ea644671a0720c85f4dbb", + "Condition_genotype_WT_KO.gprofiler2.TF.sub_enriched_pathways.tsv:md5,e272217ec7fcf01ea463ab8bcc8335cf", + "Condition_genotype_WT_KO.gprofiler2.WP.sub_enriched_pathways.tsv:md5,fdd1efa836d85bb127e933e925290cba" ] ] ], @@ -437,7 +437,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-04T14:05:08.208687138" + "timestamp": "2025-02-05T10:48:32.18827965" }, "deseq2 + gsea - mouse": { "content": [ @@ -533,10 +533,10 @@ ] ], "3": [ - + ], "4": [ - + ], "5": [ "versions.yml:md5,7861e3047b941b86ef50124168a13b51" @@ -581,10 +581,10 @@ ] ], "grea_results": [ - + ], "gsea_report": [ - + ], "versions": [ "versions.yml:md5,7861e3047b941b86ef50124168a13b51" @@ -597,4 +597,4 @@ }, "timestamp": "2025-01-24T17:38:14.74535" } -} +} \ No newline at end of file From cb18f411803d61c301b6188a9b95e838fc0c995c Mon Sep 17 00:00:00 2001 From: Suzanne Jin Date: Fri, 7 Feb 2025 15:53:23 +0000 Subject: [PATCH 11/15] fix(gprofiler2_gost): update test snapshots to match with the latest database --- .../gprofiler2/gost/tests/main.nf.test | 3 +- .../gprofiler2/gost/tests/main.nf.test.snap | 24 +++---- .../tests/all.config | 3 +- .../tests/deseq2_gprofiler2.config | 3 +- .../tests/gprofiler2.config | 3 +- .../tests/main.nf.test.snap | 64 +++++++++---------- 6 files changed, 48 insertions(+), 52 deletions(-) diff --git a/modules/nf-core/gprofiler2/gost/tests/main.nf.test b/modules/nf-core/gprofiler2/gost/tests/main.nf.test index 03bbaf64fe4..e2528ef2fe0 100644 --- a/modules/nf-core/gprofiler2/gost/tests/main.nf.test +++ b/modules/nf-core/gprofiler2/gost/tests/main.nf.test @@ -46,8 +46,7 @@ nextflow_process { ((params.gprofiler2_token == null) ? '' : "--token \"${params.gprofiler2_token}\""), ((params.gprofiler2_organism == null) ? '' : "--organism \"${params.gprofiler2_organism}\""), ((params.gprofiler2_background_column == null) ? '' : "--background_column \"${params.gprofiler2_background_column}\""), - ((params.gprofiler2_sources == null) ? '' : "--sources \"${params.gprofiler2_sources}\""), - "--archive gprofiler_archive3/e111_eg58_p18" + ((params.gprofiler2_sources == null) ? '' : "--sources \"${params.gprofiler2_sources}\"") ].join(' ').trim() } process { diff --git a/modules/nf-core/gprofiler2/gost/tests/main.nf.test.snap b/modules/nf-core/gprofiler2/gost/tests/main.nf.test.snap index 9b8920030ff..a43a1fb6304 100644 --- a/modules/nf-core/gprofiler2/gost/tests/main.nf.test.snap +++ b/modules/nf-core/gprofiler2/gost/tests/main.nf.test.snap @@ -10,7 +10,7 @@ "target": "KO", "blocking": "batch" }, - "Condition_genotype_WT_KO.gprofiler2.all_enriched_pathways.tsv:md5,1134a02ca061c463bcbff277eefbfb19" + "Condition_genotype_WT_KO.gprofiler2.all_enriched_pathways.tsv:md5,31d1e4cfa1d09b30bf9126415cb93aff" ] ], [ @@ -23,15 +23,15 @@ "blocking": "batch" }, [ - "Condition_genotype_WT_KO.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,d527b94cdb160070bcaa0bfb0cecf914", - "Condition_genotype_WT_KO.gprofiler2.GO:CC.sub_enriched_pathways.tsv:md5,ef418c3f06d50446317928e37ec8ddfb", - "Condition_genotype_WT_KO.gprofiler2.GO:MF.sub_enriched_pathways.tsv:md5,e460d4917feb0b64d334a528f59e0731", - "Condition_genotype_WT_KO.gprofiler2.HP.sub_enriched_pathways.tsv:md5,865d8f092503552831c51d775a98c6eb", + "Condition_genotype_WT_KO.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,6211f4fa1a226f3aaab77c3fb9318fe7", + "Condition_genotype_WT_KO.gprofiler2.GO:CC.sub_enriched_pathways.tsv:md5,98a49b69f8b724d88d6367dea494ca53", + "Condition_genotype_WT_KO.gprofiler2.GO:MF.sub_enriched_pathways.tsv:md5,39ce8238319df47708df78b1c461a89d", + "Condition_genotype_WT_KO.gprofiler2.HP.sub_enriched_pathways.tsv:md5,616f3a5d19844001bb8aac38049e987a", "Condition_genotype_WT_KO.gprofiler2.KEGG.sub_enriched_pathways.tsv:md5,413724002abe683f376ea914d4f21ade", - "Condition_genotype_WT_KO.gprofiler2.MIRNA.sub_enriched_pathways.tsv:md5,fce81051d7af955ddb2925ba2da9ff57", - "Condition_genotype_WT_KO.gprofiler2.REAC.sub_enriched_pathways.tsv:md5,e89e1876698ea644671a0720c85f4dbb", - "Condition_genotype_WT_KO.gprofiler2.TF.sub_enriched_pathways.tsv:md5,e272217ec7fcf01ea463ab8bcc8335cf", - "Condition_genotype_WT_KO.gprofiler2.WP.sub_enriched_pathways.tsv:md5,fdd1efa836d85bb127e933e925290cba" + "Condition_genotype_WT_KO.gprofiler2.MIRNA.sub_enriched_pathways.tsv:md5,9168f1d7f7d1b1db18a4652db05b81b6", + "Condition_genotype_WT_KO.gprofiler2.REAC.sub_enriched_pathways.tsv:md5,3571ac765c47e1c38c63c463465f2a1e", + "Condition_genotype_WT_KO.gprofiler2.TF.sub_enriched_pathways.tsv:md5,4d23e5fdc96395ea79d174b1afe84756", + "Condition_genotype_WT_KO.gprofiler2.WP.sub_enriched_pathways.tsv:md5,e99c42df912a9ee75c7197f92d615979" ] ] ], @@ -48,7 +48,7 @@ "Condition_genotype_WT_KO.gprofiler2.WP.sub_enriched_pathways.png" ], [ - + ], [ "R_sessionInfo.log" @@ -67,7 +67,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-05T10:35:35.015326132" + "timestamp": "2025-02-07T15:34:05.718473191" }, "stub": { "content": [ @@ -278,4 +278,4 @@ }, "timestamp": "2025-01-21T11:31:33.394855046" } -} +} \ No newline at end of file diff --git a/subworkflows/nf-core/differential_functional_enrichment/tests/all.config b/subworkflows/nf-core/differential_functional_enrichment/tests/all.config index 79618c1c100..7f092f0d879 100644 --- a/subworkflows/nf-core/differential_functional_enrichment/tests/all.config +++ b/subworkflows/nf-core/differential_functional_enrichment/tests/all.config @@ -45,8 +45,7 @@ process { "--round_digits 4", "--palette_name Blues", "--de_id_column gene_id", - "--organism mmusculus", - "--archive gprofiler_archive3/e111_eg58_p18" + "--organism mmusculus" ].join(' ').trim() } diff --git a/subworkflows/nf-core/differential_functional_enrichment/tests/deseq2_gprofiler2.config b/subworkflows/nf-core/differential_functional_enrichment/tests/deseq2_gprofiler2.config index 3816b40cfcf..458bb6dda14 100644 --- a/subworkflows/nf-core/differential_functional_enrichment/tests/deseq2_gprofiler2.config +++ b/subworkflows/nf-core/differential_functional_enrichment/tests/deseq2_gprofiler2.config @@ -24,8 +24,7 @@ process { "--round_digits 4", "--palette_name Blues", "--de_id_column gene_id", - "--organism mmusculus", - "--archive gprofiler_archive3/e111_eg58_p18" + "--organism mmusculus" ].join(' ').trim() } } diff --git a/subworkflows/nf-core/differential_functional_enrichment/tests/gprofiler2.config b/subworkflows/nf-core/differential_functional_enrichment/tests/gprofiler2.config index 05e24571543..1fe3a1c9b48 100644 --- a/subworkflows/nf-core/differential_functional_enrichment/tests/gprofiler2.config +++ b/subworkflows/nf-core/differential_functional_enrichment/tests/gprofiler2.config @@ -11,8 +11,7 @@ process { "--round_digits 4", "--palette_name Blues", "--de_id_column gene_id", - "--organism mmusculus", - "--archive gprofiler_archive3/e111_eg58_p18" + "--organism mmusculus" ].join(' ').trim() } } diff --git a/subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test.snap b/subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test.snap index 776f57fd6d7..b9d4a6f5ff5 100644 --- a/subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test.snap +++ b/subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "method_de": "deseq2", "method": "gprofiler2" }, - "treatment_mCherry_hND6__test.gprofiler2.all_enriched_pathways.tsv:md5,d586d92fb6cc3e41d493d14c4d9a7d92" + "treatment_mCherry_hND6__test.gprofiler2.all_enriched_pathways.tsv:md5,088003a4cbb5b6294f1c3efd7768ea6a" ], [ { @@ -56,7 +56,7 @@ "method_de": "deseq2", "method": "gprofiler2" }, - "treatment_mCherry_hND6_sample_number_test.gprofiler2.all_enriched_pathways.tsv:md5,fa880c70d06f56d8dad0ac8078e6233c" + "treatment_mCherry_hND6_sample_number_test.gprofiler2.all_enriched_pathways.tsv:md5,cd972792880248e9ad31be3fd2851a29" ], [ { @@ -101,10 +101,10 @@ "method": "gprofiler2" }, [ - "treatment_mCherry_hND6__test.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,4c95059438af872253aa95a5ff127fca", - "treatment_mCherry_hND6__test.gprofiler2.GO:CC.sub_enriched_pathways.tsv:md5,b4e4009e067f723694efc1a46a609e2b", - "treatment_mCherry_hND6__test.gprofiler2.GO:MF.sub_enriched_pathways.tsv:md5,ece72606ce6d1d037cfd5f5b198233a8", - "treatment_mCherry_hND6__test.gprofiler2.REAC.sub_enriched_pathways.tsv:md5,dc7b6f67903e25076ab95a7e1bb39bbe" + "treatment_mCherry_hND6__test.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,6047ffd74fe8a49db9b924485a441948", + "treatment_mCherry_hND6__test.gprofiler2.GO:CC.sub_enriched_pathways.tsv:md5,891018299a66d62fbe979a56e9f31035", + "treatment_mCherry_hND6__test.gprofiler2.GO:MF.sub_enriched_pathways.tsv:md5,46bb279062af777060495d56ac9767d7", + "treatment_mCherry_hND6__test.gprofiler2.REAC.sub_enriched_pathways.tsv:md5,ca5e92673eb17242477e9c2787d68323" ] ], [ @@ -120,11 +120,11 @@ "method": "gprofiler2" }, [ - "treatment_mCherry_hND6_sample_number_test.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,dc27af1c941636f8b03e8c8724773725", - "treatment_mCherry_hND6_sample_number_test.gprofiler2.GO:CC.sub_enriched_pathways.tsv:md5,09b7770d59d2efa8a58f300a16a41ae7", - "treatment_mCherry_hND6_sample_number_test.gprofiler2.GO:MF.sub_enriched_pathways.tsv:md5,a261d658ca1b1ec0511e55da734d7810", + "treatment_mCherry_hND6_sample_number_test.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,f55e010f72ee9200624137f42e94a5e5", + "treatment_mCherry_hND6_sample_number_test.gprofiler2.GO:CC.sub_enriched_pathways.tsv:md5,5bb51d9184e7257ce6cdd0ce7db16923", + "treatment_mCherry_hND6_sample_number_test.gprofiler2.GO:MF.sub_enriched_pathways.tsv:md5,210e4b99919354c79b37e12c83fdeaa5", "treatment_mCherry_hND6_sample_number_test.gprofiler2.KEGG.sub_enriched_pathways.tsv:md5,3cbdbbb1c5b232ab73d35d4a0953d19c", - "treatment_mCherry_hND6_sample_number_test.gprofiler2.REAC.sub_enriched_pathways.tsv:md5,8472cb5792bf7ec044bb95df356ad47e" + "treatment_mCherry_hND6_sample_number_test.gprofiler2.REAC.sub_enriched_pathways.tsv:md5,d754c55c2a2a1b8acda1c663165b4d2b" ] ] ], @@ -240,7 +240,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-05T11:01:43.994943675" + "timestamp": "2025-02-07T15:52:09.230720274" }, "propd + grea - mouse": { "content": [ @@ -301,7 +301,7 @@ "method_de": "deseq2", "method": "gprofiler2" }, - "treatment_mCherry_hND6__test.gprofiler2.all_enriched_pathways.tsv:md5,d586d92fb6cc3e41d493d14c4d9a7d92" + "treatment_mCherry_hND6__test.gprofiler2.all_enriched_pathways.tsv:md5,088003a4cbb5b6294f1c3efd7768ea6a" ], [ { @@ -315,7 +315,7 @@ "method_de": "deseq2", "method": "gprofiler2" }, - "treatment_mCherry_hND6_sample_number_test.gprofiler2.all_enriched_pathways.tsv:md5,fa880c70d06f56d8dad0ac8078e6233c" + "treatment_mCherry_hND6_sample_number_test.gprofiler2.all_enriched_pathways.tsv:md5,cd972792880248e9ad31be3fd2851a29" ] ], [ @@ -332,10 +332,10 @@ "method": "gprofiler2" }, [ - "treatment_mCherry_hND6__test.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,4c95059438af872253aa95a5ff127fca", - "treatment_mCherry_hND6__test.gprofiler2.GO:CC.sub_enriched_pathways.tsv:md5,b4e4009e067f723694efc1a46a609e2b", - "treatment_mCherry_hND6__test.gprofiler2.GO:MF.sub_enriched_pathways.tsv:md5,ece72606ce6d1d037cfd5f5b198233a8", - "treatment_mCherry_hND6__test.gprofiler2.REAC.sub_enriched_pathways.tsv:md5,dc7b6f67903e25076ab95a7e1bb39bbe" + "treatment_mCherry_hND6__test.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,6047ffd74fe8a49db9b924485a441948", + "treatment_mCherry_hND6__test.gprofiler2.GO:CC.sub_enriched_pathways.tsv:md5,891018299a66d62fbe979a56e9f31035", + "treatment_mCherry_hND6__test.gprofiler2.GO:MF.sub_enriched_pathways.tsv:md5,46bb279062af777060495d56ac9767d7", + "treatment_mCherry_hND6__test.gprofiler2.REAC.sub_enriched_pathways.tsv:md5,ca5e92673eb17242477e9c2787d68323" ] ], [ @@ -351,11 +351,11 @@ "method": "gprofiler2" }, [ - "treatment_mCherry_hND6_sample_number_test.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,dc27af1c941636f8b03e8c8724773725", - "treatment_mCherry_hND6_sample_number_test.gprofiler2.GO:CC.sub_enriched_pathways.tsv:md5,09b7770d59d2efa8a58f300a16a41ae7", - "treatment_mCherry_hND6_sample_number_test.gprofiler2.GO:MF.sub_enriched_pathways.tsv:md5,a261d658ca1b1ec0511e55da734d7810", + "treatment_mCherry_hND6_sample_number_test.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,f55e010f72ee9200624137f42e94a5e5", + "treatment_mCherry_hND6_sample_number_test.gprofiler2.GO:CC.sub_enriched_pathways.tsv:md5,5bb51d9184e7257ce6cdd0ce7db16923", + "treatment_mCherry_hND6_sample_number_test.gprofiler2.GO:MF.sub_enriched_pathways.tsv:md5,210e4b99919354c79b37e12c83fdeaa5", "treatment_mCherry_hND6_sample_number_test.gprofiler2.KEGG.sub_enriched_pathways.tsv:md5,3cbdbbb1c5b232ab73d35d4a0953d19c", - "treatment_mCherry_hND6_sample_number_test.gprofiler2.REAC.sub_enriched_pathways.tsv:md5,8472cb5792bf7ec044bb95df356ad47e" + "treatment_mCherry_hND6_sample_number_test.gprofiler2.REAC.sub_enriched_pathways.tsv:md5,d754c55c2a2a1b8acda1c663165b4d2b" ] ] ], @@ -379,7 +379,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-05T10:50:42.142874287" + "timestamp": "2025-02-07T15:38:37.090983694" }, "test gprofiler2 - mouse": { "content": [ @@ -393,7 +393,7 @@ "blocking": "batch", "method": "gprofiler2" }, - "Condition_genotype_WT_KO.gprofiler2.all_enriched_pathways.tsv:md5,1134a02ca061c463bcbff277eefbfb19" + "Condition_genotype_WT_KO.gprofiler2.all_enriched_pathways.tsv:md5,31d1e4cfa1d09b30bf9126415cb93aff" ] ], [ @@ -407,15 +407,15 @@ "method": "gprofiler2" }, [ - "Condition_genotype_WT_KO.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,d527b94cdb160070bcaa0bfb0cecf914", - "Condition_genotype_WT_KO.gprofiler2.GO:CC.sub_enriched_pathways.tsv:md5,ef418c3f06d50446317928e37ec8ddfb", - "Condition_genotype_WT_KO.gprofiler2.GO:MF.sub_enriched_pathways.tsv:md5,e460d4917feb0b64d334a528f59e0731", - "Condition_genotype_WT_KO.gprofiler2.HP.sub_enriched_pathways.tsv:md5,865d8f092503552831c51d775a98c6eb", + "Condition_genotype_WT_KO.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,6211f4fa1a226f3aaab77c3fb9318fe7", + "Condition_genotype_WT_KO.gprofiler2.GO:CC.sub_enriched_pathways.tsv:md5,98a49b69f8b724d88d6367dea494ca53", + "Condition_genotype_WT_KO.gprofiler2.GO:MF.sub_enriched_pathways.tsv:md5,39ce8238319df47708df78b1c461a89d", + "Condition_genotype_WT_KO.gprofiler2.HP.sub_enriched_pathways.tsv:md5,616f3a5d19844001bb8aac38049e987a", "Condition_genotype_WT_KO.gprofiler2.KEGG.sub_enriched_pathways.tsv:md5,413724002abe683f376ea914d4f21ade", - "Condition_genotype_WT_KO.gprofiler2.MIRNA.sub_enriched_pathways.tsv:md5,fce81051d7af955ddb2925ba2da9ff57", - "Condition_genotype_WT_KO.gprofiler2.REAC.sub_enriched_pathways.tsv:md5,e89e1876698ea644671a0720c85f4dbb", - "Condition_genotype_WT_KO.gprofiler2.TF.sub_enriched_pathways.tsv:md5,e272217ec7fcf01ea463ab8bcc8335cf", - "Condition_genotype_WT_KO.gprofiler2.WP.sub_enriched_pathways.tsv:md5,fdd1efa836d85bb127e933e925290cba" + "Condition_genotype_WT_KO.gprofiler2.MIRNA.sub_enriched_pathways.tsv:md5,9168f1d7f7d1b1db18a4652db05b81b6", + "Condition_genotype_WT_KO.gprofiler2.REAC.sub_enriched_pathways.tsv:md5,3571ac765c47e1c38c63c463465f2a1e", + "Condition_genotype_WT_KO.gprofiler2.TF.sub_enriched_pathways.tsv:md5,4d23e5fdc96395ea79d174b1afe84756", + "Condition_genotype_WT_KO.gprofiler2.WP.sub_enriched_pathways.tsv:md5,e99c42df912a9ee75c7197f92d615979" ] ] ], @@ -437,7 +437,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-05T10:48:32.18827965" + "timestamp": "2025-02-07T15:36:34.167491274" }, "deseq2 + gsea - mouse": { "content": [ From 5a2827ee01a1ebb1bd5f93f1ecc3bb38357c2892 Mon Sep 17 00:00:00 2001 From: Suzanne Jin Date: Wed, 12 Feb 2025 17:11:13 +0100 Subject: [PATCH 12/15] simplify ch_variance_stabilised_matrix with groupTuple() Co-authored-by: Jonathan Manning --- subworkflows/nf-core/abundance_differential_filter/main.nf | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/subworkflows/nf-core/abundance_differential_filter/main.nf b/subworkflows/nf-core/abundance_differential_filter/main.nf index d2617fb591f..8b134480e4f 100644 --- a/subworkflows/nf-core/abundance_differential_filter/main.nf +++ b/subworkflows/nf-core/abundance_differential_filter/main.nf @@ -131,10 +131,9 @@ workflow ABUNDANCE_DIFFERENTIAL_FILTER { ch_model = DESEQ2_DIFFERENTIAL.out.model .mix(LIMMA_DIFFERENTIAL.out.model) - ch_variance_stabilised_matrix = DESEQ2_NORM.out.rlog_counts.ifEmpty([[],[]]) - .mix(DESEQ2_NORM.out.vst_counts.ifEmpty([[],[]])) + ch_variance_stabilised_matrix = DESEQ2_NORM.out.rlog_counts + .mix(DESEQ2_NORM.out.vst_counts) .groupTuple() - .filter{ meta, files -> meta != [] } ch_versions = DESEQ2_DIFFERENTIAL.out.versions .mix(LIMMA_DIFFERENTIAL.out.versions) From 441d5b5df8b21f340863ace7f3c77f262db334ef Mon Sep 17 00:00:00 2001 From: Suzanne Jin Date: Thu, 13 Feb 2025 11:22:53 +0000 Subject: [PATCH 13/15] update propd container --- modules/nf-core/propr/propd/environment.yml | 2 +- modules/nf-core/propr/propd/main.nf | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/nf-core/propr/propd/environment.yml b/modules/nf-core/propr/propd/environment.yml index f6cf0b7154e..8a96cbec1bd 100644 --- a/modules/nf-core/propr/propd/environment.yml +++ b/modules/nf-core/propr/propd/environment.yml @@ -6,4 +6,4 @@ channels: dependencies: - bioconda::bioconductor-limma=3.58.1 - - conda-forge::r-propr=5.1.5 + - conda-forge::r-propr=5.1.6 diff --git a/modules/nf-core/propr/propd/main.nf b/modules/nf-core/propr/propd/main.nf index 54b81c8eb70..fb88d597829 100644 --- a/modules/nf-core/propr/propd/main.nf +++ b/modules/nf-core/propr/propd/main.nf @@ -4,8 +4,8 @@ process PROPR_PROPD { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b6/b65f7192866fbd9a947df15b104808abb720e7a224bbe3ca8f7f8f680f52c97a/data' : - 'community.wave.seqera.io/library/bioconductor-limma_r-propr:f52f1d4fea746393' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/27/276e08c149faa028a34ec65f74ac9eac58c2036a30db1f72acc9e35967936620/data' : + 'community.wave.seqera.io/library/bioconductor-limma_r-propr:8d299a2da993327c' }" input: tuple val(meta), val(contrast_variable), val(reference), val(target) From efc5e1a0b37494b892b10c683c4a4c20bf71ca42 Mon Sep 17 00:00:00 2001 From: Suzanne Jin Date: Thu, 13 Feb 2025 11:23:50 +0000 Subject: [PATCH 14/15] update differential and functional subworkflows by replacing 'method' by 'method_differential' and 'method_functional' --- .../abundance_differential_filter/main.nf | 37 ++-- .../tests/deseq2_basic.config | 4 +- .../tests/deseq2_limmavoom_basic.config | 8 +- .../tests/deseq2_limmavoom_propd_basic.config | 10 +- .../tests/limma_basic_microarray.config | 4 +- .../tests/limma_voom.config | 4 +- .../tests/main.nf.test.snap | 188 +++++++++--------- .../main.nf | 14 +- .../tests/all.config | 8 +- .../tests/deseq2_gprofiler2.config | 4 +- .../tests/deseq2_gsea.config | 4 +- .../tests/main.nf.test | 30 +-- .../tests/main.nf.test.snap | 120 +++++------ 13 files changed, 209 insertions(+), 226 deletions(-) diff --git a/subworkflows/nf-core/abundance_differential_filter/main.nf b/subworkflows/nf-core/abundance_differential_filter/main.nf index 8b134480e4f..71a3cce1fb0 100644 --- a/subworkflows/nf-core/abundance_differential_filter/main.nf +++ b/subworkflows/nf-core/abundance_differential_filter/main.nf @@ -31,8 +31,8 @@ workflow ABUNDANCE_DIFFERENTIAL_FILTER { // Set up how the channels crossed below will be used to generate channels for processing def criteria = multiMapCriteria { meta_input, abundance, analysis_method, fc_threshold, stat_threshold, meta_exp, samplesheet, meta_contrasts, variable, reference, target -> - def meta_for_diff = mergeMaps(meta_contrasts, meta_input) + [ 'method': analysis_method ] - def meta_input_new = meta_input + [ 'method': analysis_method ] + def meta_for_diff = mergeMaps(meta_contrasts, meta_input) + [ 'method_differential': analysis_method ] + def meta_input_new = meta_input + [ 'method_differential': analysis_method ] samples_and_matrix: [ meta_input_new, samplesheet, abundance ] contrasts_for_diff: @@ -71,13 +71,13 @@ workflow ABUNDANCE_DIFFERENTIAL_FILTER { // LIMMA_NORM directly. It internally runs normalization + DE analysis. LIMMA_NORM( - norm_inputs.contrasts_for_norm.filter{it[0].method == 'limma'}, - norm_inputs.samples_and_matrix.filter{it[0].method == 'limma'} + norm_inputs.contrasts_for_norm.filter{it[0].method_differential == 'limma'}, + norm_inputs.samples_and_matrix.filter{it[0].method_differential == 'limma'} ) LIMMA_DIFFERENTIAL( - inputs.contrasts_for_diff.filter{ it[0].method == 'limma' }, - inputs.samples_and_matrix.filter{ it[0].method == 'limma' } + inputs.contrasts_for_diff.filter{ it[0].method_differential == 'limma' }, + inputs.samples_and_matrix.filter{ it[0].method_differential == 'limma' } ) // ---------------------------------------------------- @@ -92,15 +92,15 @@ workflow ABUNDANCE_DIFFERENTIAL_FILTER { // DESEQ2_NORM directly. It internally runs normalization + DE analysis. DESEQ2_NORM( - norm_inputs.contrasts_for_norm.filter{it[0].method == 'deseq2'}, - norm_inputs.samples_and_matrix.filter{it[0].method == 'deseq2'}, + norm_inputs.contrasts_for_norm.filter{it[0].method_differential == 'deseq2'}, + norm_inputs.samples_and_matrix.filter{it[0].method_differential == 'deseq2'}, ch_control_features.first(), ch_transcript_lengths.first() ) DESEQ2_DIFFERENTIAL( - inputs.contrasts_for_diff.filter{it[0].method == 'deseq2'}, - inputs.samples_and_matrix.filter{it[0].method == 'deseq2'}, + inputs.contrasts_for_diff.filter{it[0].method_differential == 'deseq2'}, + inputs.samples_and_matrix.filter{it[0].method_differential == 'deseq2'}, ch_control_features.first(), ch_transcript_lengths.first() ) @@ -113,8 +113,8 @@ workflow ABUNDANCE_DIFFERENTIAL_FILTER { // not produce a normalized matrix. PROPR_PROPD( - inputs.contrasts_for_diff.filter{it[0].method == 'propd'}, - inputs.samples_and_matrix.filter { it[0].method == 'propd' } + inputs.contrasts_for_diff.filter{it[0].method_differential == 'propd'}, + inputs.samples_and_matrix.filter { it[0].method_differential == 'propd' } ) // ---------------------------------------------------- @@ -131,9 +131,10 @@ workflow ABUNDANCE_DIFFERENTIAL_FILTER { ch_model = DESEQ2_DIFFERENTIAL.out.model .mix(LIMMA_DIFFERENTIAL.out.model) - ch_variance_stabilised_matrix = DESEQ2_NORM.out.rlog_counts - .mix(DESEQ2_NORM.out.vst_counts) + ch_variance_stabilised_matrix = DESEQ2_NORM.out.rlog_counts.ifEmpty([[],[]]) + .mix(DESEQ2_NORM.out.vst_counts.ifEmpty([[],[]])) .groupTuple() + .filter{ meta, files -> meta != [] } ch_versions = DESEQ2_DIFFERENTIAL.out.versions .mix(LIMMA_DIFFERENTIAL.out.versions) @@ -162,14 +163,14 @@ workflow ABUNDANCE_DIFFERENTIAL_FILTER { ] filter_input: [meta + filter_meta, results] fc_input: [ - method_params[meta.method].fc_column, + method_params[meta.method_differential].fc_column, filter_meta.fc_threshold, - method_params[meta.method].fc_cardinality + method_params[meta.method_differential].fc_cardinality ] stat_input: [ - method_params[meta.method].stat_column, + method_params[meta.method_differential].stat_column, filter_meta.stat_threshold, - method_params[meta.method].stat_cardinality + method_params[meta.method_differential].stat_cardinality ] } diff --git a/subworkflows/nf-core/abundance_differential_filter/tests/deseq2_basic.config b/subworkflows/nf-core/abundance_differential_filter/tests/deseq2_basic.config index d6918e56f6a..4daa1a769d7 100644 --- a/subworkflows/nf-core/abundance_differential_filter/tests/deseq2_basic.config +++ b/subworkflows/nf-core/abundance_differential_filter/tests/deseq2_basic.config @@ -5,10 +5,10 @@ process { "--vs_method rlog", (meta.blocking == null) ? "" : "--blocking_variables $meta.blocking" ].join(' ').trim() } - ext.prefix = { "${meta.id}_${meta.method}" } + ext.prefix = { "${meta.id}_${meta.method_differential}" } } withName: 'DESEQ2_NORM' { - ext.prefix = { "${meta.id}_${meta.method}_norm" } + ext.prefix = { "${meta.id}_${meta.method_differential}_norm" } } } diff --git a/subworkflows/nf-core/abundance_differential_filter/tests/deseq2_limmavoom_basic.config b/subworkflows/nf-core/abundance_differential_filter/tests/deseq2_limmavoom_basic.config index 14fcfefa6dd..fbbf881f628 100644 --- a/subworkflows/nf-core/abundance_differential_filter/tests/deseq2_limmavoom_basic.config +++ b/subworkflows/nf-core/abundance_differential_filter/tests/deseq2_limmavoom_basic.config @@ -5,11 +5,11 @@ process { "--vs_method rlog", (meta.blocking == null) ? "" : "--blocking_variables $meta.blocking" ].join(' ').trim() } - ext.prefix = { "${meta.id}_${meta.method}" } + ext.prefix = { "${meta.id}_${meta.method_differential}" } } withName: 'DESEQ2_NORM' { - ext.prefix = { "${meta.id}_${meta.method}_norm" } + ext.prefix = { "${meta.id}_${meta.method_differential}_norm" } } withName: 'LIMMA_DIFFERENTIAL' { @@ -19,10 +19,10 @@ process { "--probe_id_col gene_id", "--use_voom TRUE" ].join(' ').trim() } - ext.prefix = { "${meta.id}_${meta.method}_voom" } + ext.prefix = { "${meta.id}_${meta.method_differential}_voom" } } withName: 'LIMMA_NORM' { - ext.prefix = { "${meta.id}_${meta.method}_voom_norm" } + ext.prefix = { "${meta.id}_${meta.method_differential}_voom_norm" } } } diff --git a/subworkflows/nf-core/abundance_differential_filter/tests/deseq2_limmavoom_propd_basic.config b/subworkflows/nf-core/abundance_differential_filter/tests/deseq2_limmavoom_propd_basic.config index dda5df4bcd4..b89487b0bda 100644 --- a/subworkflows/nf-core/abundance_differential_filter/tests/deseq2_limmavoom_propd_basic.config +++ b/subworkflows/nf-core/abundance_differential_filter/tests/deseq2_limmavoom_propd_basic.config @@ -5,11 +5,11 @@ process { "--vs_method rlog", (meta.blocking == null) ? "" : "--blocking_variables $meta.blocking" ].join(' ').trim() } - ext.prefix = { "${meta.id}_${meta.method}" } + ext.prefix = { "${meta.id}_${meta.method_differential}" } } withName: 'DESEQ2_NORM' { - ext.prefix = { "${meta.id}_${meta.method}_norm" } + ext.prefix = { "${meta.id}_${meta.method_differential}_norm" } } withName: 'LIMMA_DIFFERENTIAL' { @@ -19,15 +19,15 @@ process { "--probe_id_col gene_id", "--use_voom TRUE" ].join(' ').trim() } - ext.prefix = { "${meta.id}_${meta.method}_voom" } + ext.prefix = { "${meta.id}_${meta.method_differential}_voom" } } withName: 'LIMMA_NORM' { - ext.prefix = { "${meta.id}_${meta.method}_voom_norm" } + ext.prefix = { "${meta.id}_${meta.method_differential}_voom_norm" } } withName: 'PROPR_PROPD' { ext.args = {"--round_digits 5 --save_adjacency true"} - ext.prefix = { "${meta.id}_${meta.method}" } + ext.prefix = { "${meta.id}_${meta.method_differential}" } } } diff --git a/subworkflows/nf-core/abundance_differential_filter/tests/limma_basic_microarray.config b/subworkflows/nf-core/abundance_differential_filter/tests/limma_basic_microarray.config index 59eddbc362a..191a6f2e5d3 100644 --- a/subworkflows/nf-core/abundance_differential_filter/tests/limma_basic_microarray.config +++ b/subworkflows/nf-core/abundance_differential_filter/tests/limma_basic_microarray.config @@ -5,11 +5,11 @@ process { "--sample_id_col name", "--blocking_variables $meta.blocking" ].join(' ').trim() } - ext.prefix = { "${meta.id}_${meta.method}" } + ext.prefix = { "${meta.id}_${meta.method_differential}" } } withName: 'LIMMA_NORM' { - ext.prefix = { "${meta.id}_${meta.method}_norm" } + ext.prefix = { "${meta.id}_${meta.method_differential}_norm" } } withName: 'AFFY_JUSTRMA' { diff --git a/subworkflows/nf-core/abundance_differential_filter/tests/limma_voom.config b/subworkflows/nf-core/abundance_differential_filter/tests/limma_voom.config index 241679da0e5..81b144b94c1 100644 --- a/subworkflows/nf-core/abundance_differential_filter/tests/limma_voom.config +++ b/subworkflows/nf-core/abundance_differential_filter/tests/limma_voom.config @@ -8,10 +8,10 @@ process { "--use_voom TRUE" ].join(' ').trim() } - ext.prefix = { "${meta.id}_${meta.method}_voom" } + ext.prefix = { "${meta.id}_${meta.method_differential}_voom" } } withName: 'LIMMA_NORM' { - ext.prefix = { "${meta.id}_${meta.method}_voom_norm" } + ext.prefix = { "${meta.id}_${meta.method_differential}_voom_norm" } } } diff --git a/subworkflows/nf-core/abundance_differential_filter/tests/main.nf.test.snap b/subworkflows/nf-core/abundance_differential_filter/tests/main.nf.test.snap index c1b1f0ec90b..ca7ba25f884 100644 --- a/subworkflows/nf-core/abundance_differential_filter/tests/main.nf.test.snap +++ b/subworkflows/nf-core/abundance_differential_filter/tests/main.nf.test.snap @@ -8,7 +8,7 @@ "variable": "diagnosis", "reference": "normal", "target": "uremia", - "method": "limma" + "method_differential": "limma" }, "diagnosis_normal_uremia_test_limma.limma.results.tsv:md5,4f0944b54b3ab7aa6ded5dd4b4e82802" ] @@ -20,7 +20,7 @@ "variable": "diagnosis", "reference": "normal", "target": "uremia", - "method": "limma", + "method_differential": "limma", "fc_threshold": 1.5, "stat_threshold": 0.05 }, @@ -28,7 +28,7 @@ ] ], [ - + ], [ [ @@ -37,7 +37,7 @@ "variable": "diagnosis", "reference": "normal", "target": "uremia", - "method": "limma" + "method_differential": "limma" }, "diagnosis_normal_uremia_test_limma.limma.model.txt:md5,70b000f632b8bdba4917046362dd876b" ] @@ -50,7 +50,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-04T13:54:29.394126445" + "timestamp": "2025-02-13T10:34:11.577546081" }, "deseq2 and limma - mouse - basic": { "content": [ @@ -62,7 +62,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "", - "method": "deseq2" + "method_differential": "deseq2" }, "treatment_mCherry_hND6__test_deseq2.deseq2.results.tsv:md5,791cdba2615a445cded13cae95df73ef" ], @@ -73,7 +73,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "", - "method": "limma" + "method_differential": "limma" }, "treatment_mCherry_hND6__test_limma_voom.limma.results.tsv:md5,ff36827b7869a8a3c3c905efedcafc93" ], @@ -84,7 +84,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "sample_number", - "method": "deseq2" + "method_differential": "deseq2" }, "treatment_mCherry_hND6_sample_number_test_deseq2.deseq2.results.tsv:md5,2438053a4bdc869f467a12d3c22c7ba7" ], @@ -95,7 +95,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "sample_number", - "method": "limma" + "method_differential": "limma" }, "treatment_mCherry_hND6_sample_number_test_limma_voom.limma.results.tsv:md5,5f34e79dbcb5ba1908d797548921d7fc" ] @@ -108,7 +108,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "", - "method": "deseq2", + "method_differential": "deseq2", "fc_threshold": 1.5, "stat_threshold": 0.05 }, @@ -121,7 +121,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "", - "method": "limma", + "method_differential": "limma", "fc_threshold": 1.5, "stat_threshold": 0.05 }, @@ -134,7 +134,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "sample_number", - "method": "deseq2", + "method_differential": "deseq2", "fc_threshold": 1.5, "stat_threshold": 0.05 }, @@ -147,7 +147,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "sample_number", - "method": "limma", + "method_differential": "limma", "fc_threshold": 1.5, "stat_threshold": 0.05 }, @@ -158,14 +158,14 @@ [ { "id": "test", - "method": "deseq2" + "method_differential": "deseq2" }, "test_deseq2_norm.normalised_counts.tsv:md5,46ab7200c626649ab6256ed797ef5071" ], [ { "id": "test", - "method": "limma" + "method_differential": "limma" }, "test_limma_voom_norm.normalised_counts.tsv:md5,2aa4880ba5ae246a728b25f4316ca2ca" ] @@ -174,7 +174,7 @@ [ { "id": "test", - "method": "deseq2" + "method_differential": "deseq2" }, [ "test_deseq2_norm.rlog.tsv:md5,b1adc1fba6bd0c8b55973608f4b97030" @@ -189,7 +189,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "", - "method": "deseq2" + "method_differential": "deseq2" }, "treatment_mCherry_hND6__test_deseq2.deseq2.model.txt:md5,d2113d82b76046c319e6602da2ad74d6" ], @@ -200,7 +200,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "", - "method": "limma" + "method_differential": "limma" }, "treatment_mCherry_hND6__test_limma_voom.limma.model.txt:md5,d2113d82b76046c319e6602da2ad74d6" ], @@ -211,7 +211,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "sample_number", - "method": "deseq2" + "method_differential": "deseq2" }, "treatment_mCherry_hND6_sample_number_test_deseq2.deseq2.model.txt:md5,fa05126a58cb67c107d45426b0bdea83" ], @@ -222,7 +222,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "sample_number", - "method": "limma" + "method_differential": "limma" }, "treatment_mCherry_hND6_sample_number_test_limma_voom.limma.model.txt:md5,3b96713b4e3f027b0347859f02a9038d" ] @@ -238,7 +238,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-04T13:56:48.852994235" + "timestamp": "2025-02-13T10:36:58.093453556" }, "limma - voom": { "content": [ @@ -250,7 +250,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "", - "method": "limma", + "method_differential": "limma", "fc_threshold": 1.5, "stat_threshold": 0.05 }, @@ -263,7 +263,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "sample_number", - "method": "limma", + "method_differential": "limma", "fc_threshold": 1.5, "stat_threshold": 0.05 }, @@ -274,7 +274,7 @@ [ { "id": "test", - "method": "limma" + "method_differential": "limma" }, "test_limma_voom_norm.normalised_counts.tsv:md5,2aa4880ba5ae246a728b25f4316ca2ca" ] @@ -287,7 +287,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "", - "method": "limma" + "method_differential": "limma" }, "treatment_mCherry_hND6__test_limma_voom.limma.model.txt:md5,d2113d82b76046c319e6602da2ad74d6" ], @@ -298,7 +298,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "sample_number", - "method": "limma" + "method_differential": "limma" }, "treatment_mCherry_hND6_sample_number_test_limma_voom.limma.model.txt:md5,3b96713b4e3f027b0347859f02a9038d" ] @@ -312,7 +312,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-04T13:54:49.182493737" + "timestamp": "2025-02-13T10:34:30.079348808" }, "deseq2 + limma-voom + propd - mouse - basic": { "content": [ @@ -324,7 +324,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "", - "method": "deseq2" + "method_differential": "deseq2" }, "treatment_mCherry_hND6__test_deseq2.deseq2.results.tsv:md5,791cdba2615a445cded13cae95df73ef" ], @@ -335,7 +335,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "", - "method": "limma" + "method_differential": "limma" }, "treatment_mCherry_hND6__test_limma_voom.limma.results.tsv:md5,ff36827b7869a8a3c3c905efedcafc93" ], @@ -346,7 +346,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "", - "method": "propd" + "method_differential": "propd" }, "treatment_mCherry_hND6__test_propd.propd.genewise.tsv:md5,bdc19a4b7430f248cd332287b630c872" ], @@ -357,7 +357,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "sample_number", - "method": "deseq2" + "method_differential": "deseq2" }, "treatment_mCherry_hND6_sample_number_test_deseq2.deseq2.results.tsv:md5,2438053a4bdc869f467a12d3c22c7ba7" ], @@ -368,7 +368,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "sample_number", - "method": "limma" + "method_differential": "limma" }, "treatment_mCherry_hND6_sample_number_test_limma_voom.limma.results.tsv:md5,5f34e79dbcb5ba1908d797548921d7fc" ], @@ -379,7 +379,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "sample_number", - "method": "propd" + "method_differential": "propd" }, "treatment_mCherry_hND6_sample_number_test_propd.propd.genewise.tsv:md5,bdc19a4b7430f248cd332287b630c872" ] @@ -392,7 +392,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "", - "method": "deseq2", + "method_differential": "deseq2", "fc_threshold": 1.5, "stat_threshold": 0.05 }, @@ -405,7 +405,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "", - "method": "limma", + "method_differential": "limma", "fc_threshold": 1.5, "stat_threshold": 0.05 }, @@ -418,7 +418,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "", - "method": "propd", + "method_differential": "propd", "fc_threshold": 1.5, "stat_threshold": 100 }, @@ -431,7 +431,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "sample_number", - "method": "deseq2", + "method_differential": "deseq2", "fc_threshold": 1.5, "stat_threshold": 0.05 }, @@ -444,7 +444,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "sample_number", - "method": "limma", + "method_differential": "limma", "fc_threshold": 1.5, "stat_threshold": 0.05 }, @@ -457,7 +457,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "sample_number", - "method": "propd", + "method_differential": "propd", "fc_threshold": 1.5, "stat_threshold": 100 }, @@ -472,7 +472,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "", - "method": "propd" + "method_differential": "propd" }, "treatment_mCherry_hND6__test_propd.propd.adjacency.csv:md5,3a947ffd8172990c6207aa7561a41cb8" ], @@ -483,7 +483,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "sample_number", - "method": "propd" + "method_differential": "propd" }, "treatment_mCherry_hND6_sample_number_test_propd.propd.adjacency.csv:md5,3a947ffd8172990c6207aa7561a41cb8" ] @@ -492,14 +492,14 @@ [ { "id": "test", - "method": "deseq2" + "method_differential": "deseq2" }, "test_deseq2_norm.normalised_counts.tsv:md5,46ab7200c626649ab6256ed797ef5071" ], [ { "id": "test", - "method": "limma" + "method_differential": "limma" }, "test_limma_voom_norm.normalised_counts.tsv:md5,2aa4880ba5ae246a728b25f4316ca2ca" ] @@ -508,7 +508,7 @@ [ { "id": "test", - "method": "deseq2" + "method_differential": "deseq2" }, [ "test_deseq2_norm.rlog.tsv:md5,b1adc1fba6bd0c8b55973608f4b97030" @@ -523,7 +523,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "", - "method": "deseq2" + "method_differential": "deseq2" }, "treatment_mCherry_hND6__test_deseq2.deseq2.model.txt:md5,d2113d82b76046c319e6602da2ad74d6" ], @@ -534,7 +534,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "", - "method": "limma" + "method_differential": "limma" }, "treatment_mCherry_hND6__test_limma_voom.limma.model.txt:md5,d2113d82b76046c319e6602da2ad74d6" ], @@ -545,7 +545,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "sample_number", - "method": "deseq2" + "method_differential": "deseq2" }, "treatment_mCherry_hND6_sample_number_test_deseq2.deseq2.model.txt:md5,fa05126a58cb67c107d45426b0bdea83" ], @@ -556,7 +556,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "sample_number", - "method": "limma" + "method_differential": "limma" }, "treatment_mCherry_hND6_sample_number_test_limma_voom.limma.model.txt:md5,3b96713b4e3f027b0347859f02a9038d" ] @@ -574,7 +574,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-04T13:57:45.650163566" + "timestamp": "2025-02-13T10:38:17.764737776" }, "stub": { "content": [ @@ -587,7 +587,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "", - "method": "deseq2" + "method_differential": "deseq2" }, "treatment_mCherry_hND6__test.deseq2.results.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ], @@ -598,7 +598,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "sample_number", - "method": "deseq2" + "method_differential": "deseq2" }, "treatment_mCherry_hND6_sample_number_test.deseq2.results.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -611,7 +611,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "", - "method": "deseq2", + "method_differential": "deseq2", "fc_threshold": 1.5, "stat_threshold": 0.05 }, @@ -624,7 +624,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "sample_number", - "method": "deseq2", + "method_differential": "deseq2", "fc_threshold": 1.5, "stat_threshold": 0.05 }, @@ -632,13 +632,13 @@ ] ], "2": [ - + ], "3": [ [ { "id": "test", - "method": "deseq2" + "method_differential": "deseq2" }, "test.normalised_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -647,7 +647,7 @@ [ { "id": "test", - "method": "deseq2" + "method_differential": "deseq2" }, [ "test.rlog.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -662,7 +662,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "", - "method": "deseq2" + "method_differential": "deseq2" }, "treatment_mCherry_hND6__test.deseq2.model.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ], @@ -673,7 +673,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "sample_number", - "method": "deseq2" + "method_differential": "deseq2" }, "treatment_mCherry_hND6_sample_number_test.deseq2.model.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -683,7 +683,7 @@ "versions.yml:md5,05e3901f6d78f8839a7e07f422e9bc03" ], "adjacency": [ - + ], "model": [ [ @@ -693,7 +693,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "", - "method": "deseq2" + "method_differential": "deseq2" }, "treatment_mCherry_hND6__test.deseq2.model.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ], @@ -704,7 +704,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "sample_number", - "method": "deseq2" + "method_differential": "deseq2" }, "treatment_mCherry_hND6_sample_number_test.deseq2.model.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -713,7 +713,7 @@ [ { "id": "test", - "method": "deseq2" + "method_differential": "deseq2" }, "test.normalised_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -726,7 +726,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "", - "method": "deseq2" + "method_differential": "deseq2" }, "treatment_mCherry_hND6__test.deseq2.results.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ], @@ -737,7 +737,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "sample_number", - "method": "deseq2" + "method_differential": "deseq2" }, "treatment_mCherry_hND6_sample_number_test.deseq2.results.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -750,7 +750,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "", - "method": "deseq2", + "method_differential": "deseq2", "fc_threshold": 1.5, "stat_threshold": 0.05 }, @@ -763,7 +763,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "sample_number", - "method": "deseq2", + "method_differential": "deseq2", "fc_threshold": 1.5, "stat_threshold": 0.05 }, @@ -774,7 +774,7 @@ [ { "id": "test", - "method": "deseq2" + "method_differential": "deseq2" }, [ "test.rlog.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -791,7 +791,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-04T13:58:07.872952803" + "timestamp": "2025-02-13T10:38:39.583037677" }, "deseq2 - mouse - basic": { "content": [ @@ -803,7 +803,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "", - "method": "deseq2" + "method_differential": "deseq2" }, "treatment_mCherry_hND6__test_deseq2.deseq2.results.tsv:md5,791cdba2615a445cded13cae95df73ef" ], @@ -814,7 +814,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "sample_number", - "method": "deseq2" + "method_differential": "deseq2" }, "treatment_mCherry_hND6_sample_number_test_deseq2.deseq2.results.tsv:md5,2438053a4bdc869f467a12d3c22c7ba7" ] @@ -827,7 +827,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "", - "method": "deseq2", + "method_differential": "deseq2", "fc_threshold": 1.5, "stat_threshold": 0.05 }, @@ -840,7 +840,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "sample_number", - "method": "deseq2", + "method_differential": "deseq2", "fc_threshold": 1.5, "stat_threshold": 0.05 }, @@ -851,7 +851,7 @@ [ { "id": "test", - "method": "deseq2" + "method_differential": "deseq2" }, "test_deseq2_norm.normalised_counts.tsv:md5,46ab7200c626649ab6256ed797ef5071" ] @@ -860,7 +860,7 @@ [ { "id": "test", - "method": "deseq2" + "method_differential": "deseq2" }, [ "test_deseq2_norm.rlog.tsv:md5,b1adc1fba6bd0c8b55973608f4b97030" @@ -875,7 +875,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "", - "method": "deseq2" + "method_differential": "deseq2" }, "treatment_mCherry_hND6__test_deseq2.deseq2.model.txt:md5,d2113d82b76046c319e6602da2ad74d6" ], @@ -886,7 +886,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "sample_number", - "method": "deseq2" + "method_differential": "deseq2" }, "treatment_mCherry_hND6_sample_number_test_deseq2.deseq2.model.txt:md5,fa05126a58cb67c107d45426b0bdea83" ] @@ -900,7 +900,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-04T13:53:33.612999183" + "timestamp": "2025-02-13T10:32:38.95991796" }, "deseq2 - with transcript lengths": { "content": [ @@ -912,7 +912,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "", - "method": "deseq2" + "method_differential": "deseq2" }, "treatment_mCherry_hND6__test_deseq2.deseq2.results.tsv:md5,944176b73455aa7c8de3ec32c03edef6" ], @@ -923,7 +923,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "sample_number", - "method": "deseq2" + "method_differential": "deseq2" }, "treatment_mCherry_hND6_sample_number_test_deseq2.deseq2.results.tsv:md5,6a9bc76c9d54034c90fa159372f97516" ] @@ -936,7 +936,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "", - "method": "deseq2", + "method_differential": "deseq2", "fc_threshold": 1.5, "stat_threshold": 0.05 }, @@ -949,7 +949,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "sample_number", - "method": "deseq2", + "method_differential": "deseq2", "fc_threshold": 1.5, "stat_threshold": 0.05 }, @@ -960,7 +960,7 @@ [ { "id": "test", - "method": "deseq2" + "method_differential": "deseq2" }, "test_deseq2_norm.normalised_counts.tsv:md5,7050f44c460cc13e3f101d048d503527" ] @@ -969,7 +969,7 @@ [ { "id": "test", - "method": "deseq2" + "method_differential": "deseq2" }, [ "test_deseq2_norm.rlog.tsv:md5,22a4b117246b2317e0f4daf7919703f2" @@ -984,7 +984,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "", - "method": "deseq2" + "method_differential": "deseq2" }, "treatment_mCherry_hND6__test_deseq2.deseq2.model.txt:md5,d2113d82b76046c319e6602da2ad74d6" ], @@ -995,7 +995,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "sample_number", - "method": "deseq2" + "method_differential": "deseq2" }, "treatment_mCherry_hND6_sample_number_test_deseq2.deseq2.model.txt:md5,fa05126a58cb67c107d45426b0bdea83" ] @@ -1009,7 +1009,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-04T13:55:36.036520174" + "timestamp": "2025-02-13T10:35:17.824545735" }, "propd - mouse - basic": { "content": [ @@ -1021,7 +1021,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "", - "method": "propd" + "method_differential": "propd" }, "treatment_mCherry_hND6__test.propd.genewise.tsv:md5,bdc19a4b7430f248cd332287b630c872" ], @@ -1032,7 +1032,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "sample_number", - "method": "propd" + "method_differential": "propd" }, "treatment_mCherry_hND6_sample_number_test.propd.genewise.tsv:md5,bdc19a4b7430f248cd332287b630c872" ] @@ -1045,7 +1045,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "", - "method": "propd", + "method_differential": "propd", "fc_threshold": 1.5, "stat_threshold": 100 }, @@ -1058,7 +1058,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "sample_number", - "method": "propd", + "method_differential": "propd", "fc_threshold": 1.5, "stat_threshold": 100 }, @@ -1073,7 +1073,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "", - "method": "propd" + "method_differential": "propd" }, "treatment_mCherry_hND6__test.propd.adjacency.csv:md5,3a947ffd8172990c6207aa7561a41cb8" ], @@ -1084,7 +1084,7 @@ "reference": "mCherry", "target": "hND6", "blocking": "sample_number", - "method": "propd" + "method_differential": "propd" }, "treatment_mCherry_hND6_sample_number_test.propd.adjacency.csv:md5,3a947ffd8172990c6207aa7561a41cb8" ] @@ -1098,6 +1098,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-04T13:55:58.53500005" + "timestamp": "2025-02-13T10:35:58.616740674" } -} \ No newline at end of file +} diff --git a/subworkflows/nf-core/differential_functional_enrichment/main.nf b/subworkflows/nf-core/differential_functional_enrichment/main.nf index ff18aedc0f6..802812a5d93 100644 --- a/subworkflows/nf-core/differential_functional_enrichment/main.nf +++ b/subworkflows/nf-core/differential_functional_enrichment/main.nf @@ -41,7 +41,7 @@ workflow DIFFERENTIAL_FUNCTIONAL_ENRICHMENT { ch_input = ch_input .multiMap { meta_input, file, genesets, background, analysis_method -> - def meta_new = meta_input + [ 'method': analysis_method ] + def meta_new = meta_input + [ 'method_functional': analysis_method ] input: [ meta_new, file ] genesets: @@ -69,7 +69,7 @@ workflow DIFFERENTIAL_FUNCTIONAL_ENRICHMENT { } ch_preinput_for_gsea = ch_input.input .join(ch_input.genesets) - .filter{ it[0].method == 'gsea' } + .filter{ it[0].method_functional == 'gsea' } .combine(ch_samplesheet.join(ch_featuresheet)) .combine(ch_contrasts) .multiMap(criteria) @@ -79,9 +79,9 @@ workflow DIFFERENTIAL_FUNCTIONAL_ENRICHMENT { // ---------------------------------------------------- GPROFILER2_GOST( - ch_input.input.filter{ it[0].method == 'gprofiler2' }, - ch_input.genesets.filter{ it[0].method == 'gprofiler2'}, - ch_input.background.filter{ it[0].method == 'gprofiler2'} + ch_input.input.filter{ it[0].method_functional == 'gprofiler2' }, + ch_input.genesets.filter{ it[0].method_functional == 'gprofiler2'}, + ch_input.background.filter{ it[0].method_functional == 'gprofiler2'} ) // ---------------------------------------------------- @@ -116,8 +116,8 @@ workflow DIFFERENTIAL_FUNCTIONAL_ENRICHMENT { // ---------------------------------------------------- PROPR_GREA( - ch_input.input.filter{ it[0].method == 'grea' }, - ch_input.genesets.filter{ it[0].method == 'grea' } + ch_input.input.filter{ it[0].method_functional == 'grea' }, + ch_input.genesets.filter{ it[0].method_functional == 'grea' } ) // collect versions info diff --git a/subworkflows/nf-core/differential_functional_enrichment/tests/all.config b/subworkflows/nf-core/differential_functional_enrichment/tests/all.config index 7f092f0d879..eb32d8ca4bb 100644 --- a/subworkflows/nf-core/differential_functional_enrichment/tests/all.config +++ b/subworkflows/nf-core/differential_functional_enrichment/tests/all.config @@ -8,11 +8,11 @@ process { "--vs_method rlog", (meta.blocking == null) ? "" : "--blocking_variables $meta.blocking" ].join(' ').trim() } - ext.prefix = { "${meta.id}_${meta.method}" } + ext.prefix = { "${meta.id}_${meta.method_differential}" } } withName: 'DESEQ2_NORM' { - ext.prefix = { "${meta.id}_${meta.method}_norm --round_digits 5" } + ext.prefix = { "${meta.id}_${meta.method_differential}_norm" } } withName: 'LIMMA_DIFFERENTIAL' { @@ -22,11 +22,11 @@ process { "--probe_id_col gene_id", "--use_voom TRUE" ].join(' ').trim() } - ext.prefix = { "${meta.id}_${meta.method}_voom" } + ext.prefix = { "${meta.id}_${meta.method_differential}_voom" } } withName: 'LIMMA_NORM' { - ext.prefix = { "${meta.id}_${meta.method}_voom_norm" } + ext.prefix = { "${meta.id}_${meta.method_differential}_voom_norm" } } withName: "PROPR_PROPD"{ diff --git a/subworkflows/nf-core/differential_functional_enrichment/tests/deseq2_gprofiler2.config b/subworkflows/nf-core/differential_functional_enrichment/tests/deseq2_gprofiler2.config index 458bb6dda14..80e36b6167a 100644 --- a/subworkflows/nf-core/differential_functional_enrichment/tests/deseq2_gprofiler2.config +++ b/subworkflows/nf-core/differential_functional_enrichment/tests/deseq2_gprofiler2.config @@ -5,11 +5,11 @@ process { "--vs_method rlog", (meta.blocking == null) ? "" : "--blocking_variables $meta.blocking" ].join(' ').trim() } - ext.prefix = { "${meta.id}_${meta.method}" } + ext.prefix = { "${meta.id}_${meta.method_differential}" } } withName: 'DESEQ2_NORM' { - ext.prefix = { "${meta.id}_${meta.method}_norm --round_digits 5" } + ext.prefix = { "${meta.id}_${meta.method_differential}_norm" } } withName: 'GPROFILER2_GOST' { diff --git a/subworkflows/nf-core/differential_functional_enrichment/tests/deseq2_gsea.config b/subworkflows/nf-core/differential_functional_enrichment/tests/deseq2_gsea.config index 4ec648e6cb8..613eaba2764 100644 --- a/subworkflows/nf-core/differential_functional_enrichment/tests/deseq2_gsea.config +++ b/subworkflows/nf-core/differential_functional_enrichment/tests/deseq2_gsea.config @@ -5,11 +5,11 @@ process { "--vs_method rlog", (meta.blocking == null) ? "" : "--blocking_variables $meta.blocking" ].join(' ').trim() } - ext.prefix = { "${meta.id}_${meta.method}" } + ext.prefix = { "${meta.id}_${meta.method_differential}" } } withName: 'DESEQ2_NORM' { - ext.prefix = { "${meta.id}_${meta.method}_norm --round_digits 5" } + ext.prefix = { "${meta.id}_${meta.method_differential}_norm" } } withName: 'CUSTOM_TABULARTOGSEACLS' { diff --git a/subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test b/subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test index bb01beb8e80..5fc454490bf 100644 --- a/subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test +++ b/subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test @@ -108,9 +108,7 @@ nextflow_workflow { """ ch_input = ABUNDANCE_DIFFERENTIAL_FILTER.out.results_genewise_filtered .map { meta, results -> - def meta_new = meta - ['method': meta.method] - meta_new.method_de = meta.method - [meta_new, results, [], [], 'gprofiler2'] + [meta, results, [], [], 'gprofiler2'] } input[0] = ch_input @@ -198,9 +196,7 @@ nextflow_workflow { ch_input = ABUNDANCE_DIFFERENTIAL_FILTER.out.normalised_matrix .combine(Channel.fromPath(testData.genesets_file)) .map { meta, matrix, genesets -> - def meta_new = meta - ['method': meta.method] - meta_new.method_de = meta.method - [meta_new, matrix, genesets, [], 'gsea'] + [meta, matrix, genesets, [], 'gsea'] } ch_contrasts = Channel.fromPath(file(testData.contrasts_file)) .splitCsv ( header:true, sep:',' ) @@ -291,9 +287,7 @@ nextflow_workflow { ch_input = ABUNDANCE_DIFFERENTIAL_FILTER.out.adjacency .combine(Channel.fromPath(params.modules_testdata_base_path + 'genomics/mus_musculus/gene_set_analysis/mh.all.v2022.1.Mm.symbols.gmt')) .map { meta, results, genesets -> - def meta_new = meta - ['method': meta.method] - meta_new.method_de = meta.method - [meta_new, results, genesets, [], 'grea'] + [meta, results, genesets, [], 'grea'] } input[0] = ch_input @@ -393,23 +387,11 @@ nextflow_workflow { // define input channels ch_input_for_gprofiler2 = ABUNDANCE_DIFFERENTIAL_FILTER.out.results_genewise_filtered - .map { meta, results -> - def meta_new = meta - ['method': meta.method] - meta_new.method_de = meta.method - [meta_new, results, 'gprofiler2'] - } + .combine(Channel.of('gprofiler2')) ch_input_for_gsea = ABUNDANCE_DIFFERENTIAL_FILTER.out.normalised_matrix - .map { meta, results -> - def meta_new = meta - ['method': meta.method] - meta_new.method_de = meta.method - [meta_new, results, 'gsea'] - } + .combine(Channel.of('gsea')) ch_input_for_grea = ABUNDANCE_DIFFERENTIAL_FILTER.out.adjacency - .map { meta, results -> - def meta_new = meta - ['method': meta.method] - meta_new.method_de = meta.method - [meta_new, results, 'grea'] - } + .combine(Channel.of('grea')) ch_input = ch_input_for_gprofiler2 .mix(ch_input_for_gsea) .mix(ch_input_for_grea) diff --git a/subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test.snap b/subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test.snap index b9d4a6f5ff5..f695dcf0597 100644 --- a/subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test.snap +++ b/subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test.snap @@ -9,10 +9,10 @@ "reference": "mCherry", "target": "hND6", "blocking": "", + "method_differential": "deseq2", "fc_threshold": 1.5, "stat_threshold": 0.05, - "method_de": "deseq2", - "method": "gprofiler2" + "method_functional": "gprofiler2" }, "treatment_mCherry_hND6__test.gprofiler2.all_enriched_pathways.tsv:md5,088003a4cbb5b6294f1c3efd7768ea6a" ], @@ -23,10 +23,10 @@ "reference": "mCherry", "target": "hND6", "blocking": "", + "method_differential": "limma", "fc_threshold": 1.5, "stat_threshold": 0.05, - "method_de": "limma", - "method": "gprofiler2" + "method_functional": "gprofiler2" }, "treatment_mCherry_hND6__test.gprofiler2.all_enriched_pathways.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ], @@ -37,10 +37,10 @@ "reference": "mCherry", "target": "hND6", "blocking": "", + "method_differential": "propd", "fc_threshold": 1.5, "stat_threshold": 100, - "method_de": "propd", - "method": "gprofiler2" + "method_functional": "gprofiler2" }, "treatment_mCherry_hND6__test.gprofiler2.all_enriched_pathways.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ], @@ -51,10 +51,10 @@ "reference": "mCherry", "target": "hND6", "blocking": "sample_number", + "method_differential": "deseq2", "fc_threshold": 1.5, "stat_threshold": 0.05, - "method_de": "deseq2", - "method": "gprofiler2" + "method_functional": "gprofiler2" }, "treatment_mCherry_hND6_sample_number_test.gprofiler2.all_enriched_pathways.tsv:md5,cd972792880248e9ad31be3fd2851a29" ], @@ -65,10 +65,10 @@ "reference": "mCherry", "target": "hND6", "blocking": "sample_number", + "method_differential": "limma", "fc_threshold": 1.5, "stat_threshold": 0.05, - "method_de": "limma", - "method": "gprofiler2" + "method_functional": "gprofiler2" }, "treatment_mCherry_hND6_sample_number_test.gprofiler2.all_enriched_pathways.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ], @@ -79,10 +79,10 @@ "reference": "mCherry", "target": "hND6", "blocking": "sample_number", + "method_differential": "propd", "fc_threshold": 1.5, "stat_threshold": 100, - "method_de": "propd", - "method": "gprofiler2" + "method_functional": "gprofiler2" }, "treatment_mCherry_hND6_sample_number_test.gprofiler2.all_enriched_pathways.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -95,10 +95,10 @@ "reference": "mCherry", "target": "hND6", "blocking": "", + "method_differential": "deseq2", "fc_threshold": 1.5, "stat_threshold": 0.05, - "method_de": "deseq2", - "method": "gprofiler2" + "method_functional": "gprofiler2" }, [ "treatment_mCherry_hND6__test.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,6047ffd74fe8a49db9b924485a441948", @@ -114,10 +114,10 @@ "reference": "mCherry", "target": "hND6", "blocking": "sample_number", + "method_differential": "deseq2", "fc_threshold": 1.5, "stat_threshold": 0.05, - "method_de": "deseq2", - "method": "gprofiler2" + "method_functional": "gprofiler2" }, [ "treatment_mCherry_hND6_sample_number_test.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,f55e010f72ee9200624137f42e94a5e5", @@ -140,8 +140,8 @@ "reference": "mCherry", "target": "hND6", "blocking": "", - "method_de": "deseq2", - "method": "gsea" + "method_differential": "deseq2", + "method_functional": "gsea" }, "treatment_mCherry_hND6__test.mh.all.v2022.1.Mm.symbols.gsea_report_for_mCherry.tsv:md5,ce8792382ae299749445767ff16aaecc", "treatment_mCherry_hND6__test.mh.all.v2022.1.Mm.symbols.gsea_report_for_hND6.tsv:md5,354a961c7e1417db2bf1f7e8d00c54f0" @@ -153,8 +153,8 @@ "reference": "mCherry", "target": "hND6", "blocking": "", - "method_de": "limma", - "method": "gsea" + "method_differential": "limma", + "method_functional": "gsea" }, "treatment_mCherry_hND6__test.mh.all.v2022.1.Mm.symbols.gsea_report_for_mCherry.tsv:md5,ce8792382ae299749445767ff16aaecc", "treatment_mCherry_hND6__test.mh.all.v2022.1.Mm.symbols.gsea_report_for_hND6.tsv:md5,a4dcc9581c9c63d35ef32ee0df882074" @@ -166,8 +166,8 @@ "reference": "mCherry", "target": "hND6", "blocking": "sample_number", - "method_de": "deseq2", - "method": "gsea" + "method_differential": "deseq2", + "method_functional": "gsea" }, "treatment_mCherry_hND6_sample_number_test.mh.all.v2022.1.Mm.symbols.gsea_report_for_mCherry.tsv:md5,ce8792382ae299749445767ff16aaecc", "treatment_mCherry_hND6_sample_number_test.mh.all.v2022.1.Mm.symbols.gsea_report_for_hND6.tsv:md5,354a961c7e1417db2bf1f7e8d00c54f0" @@ -179,8 +179,8 @@ "reference": "mCherry", "target": "hND6", "blocking": "sample_number", - "method_de": "limma", - "method": "gsea" + "method_differential": "limma", + "method_functional": "gsea" }, "treatment_mCherry_hND6_sample_number_test.mh.all.v2022.1.Mm.symbols.gsea_report_for_mCherry.tsv:md5,ce8792382ae299749445767ff16aaecc", "treatment_mCherry_hND6_sample_number_test.mh.all.v2022.1.Mm.symbols.gsea_report_for_hND6.tsv:md5,a4dcc9581c9c63d35ef32ee0df882074" @@ -194,8 +194,8 @@ "reference": "mCherry", "target": "hND6", "blocking": "", - "method_de": "propd", - "method": "grea" + "method_differential": "propd", + "method_functional": "grea" }, "treatment_mCherry_hND6__test.grea.tsv:md5,786faeccf39926d2f7c980ef549a2697" ], @@ -206,8 +206,8 @@ "reference": "mCherry", "target": "hND6", "blocking": "sample_number", - "method_de": "propd", - "method": "grea" + "method_differential": "propd", + "method_functional": "grea" }, "treatment_mCherry_hND6_sample_number_test.grea.tsv:md5,786faeccf39926d2f7c980ef549a2697" ] @@ -240,7 +240,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-07T15:52:09.230720274" + "timestamp": "2025-02-13T11:20:49.22761506" }, "propd + grea - mouse": { "content": [ @@ -252,8 +252,8 @@ "reference": "mCherry", "target": "hND6", "blocking": "", - "method_de": "propd", - "method": "grea" + "method_differential": "propd", + "method_functional": "grea" }, "treatment_mCherry_hND6__test.grea.tsv:md5,786faeccf39926d2f7c980ef549a2697" ], @@ -264,8 +264,8 @@ "reference": "mCherry", "target": "hND6", "blocking": "sample_number", - "method_de": "propd", - "method": "grea" + "method_differential": "propd", + "method_functional": "grea" }, "treatment_mCherry_hND6_sample_number_test.grea.tsv:md5,786faeccf39926d2f7c980ef549a2697" ] @@ -284,7 +284,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-04T14:08:03.665178563" + "timestamp": "2025-02-13T10:45:12.878451415" }, "deseq2 + gprofiler2 - mouse": { "content": [ @@ -296,10 +296,10 @@ "reference": "mCherry", "target": "hND6", "blocking": "", + "method_differential": "deseq2", "fc_threshold": 1.5, "stat_threshold": 0.05, - "method_de": "deseq2", - "method": "gprofiler2" + "method_functional": "gprofiler2" }, "treatment_mCherry_hND6__test.gprofiler2.all_enriched_pathways.tsv:md5,088003a4cbb5b6294f1c3efd7768ea6a" ], @@ -310,10 +310,10 @@ "reference": "mCherry", "target": "hND6", "blocking": "sample_number", + "method_differential": "deseq2", "fc_threshold": 1.5, "stat_threshold": 0.05, - "method_de": "deseq2", - "method": "gprofiler2" + "method_functional": "gprofiler2" }, "treatment_mCherry_hND6_sample_number_test.gprofiler2.all_enriched_pathways.tsv:md5,cd972792880248e9ad31be3fd2851a29" ] @@ -326,10 +326,10 @@ "reference": "mCherry", "target": "hND6", "blocking": "", + "method_differential": "deseq2", "fc_threshold": 1.5, "stat_threshold": 0.05, - "method_de": "deseq2", - "method": "gprofiler2" + "method_functional": "gprofiler2" }, [ "treatment_mCherry_hND6__test.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,6047ffd74fe8a49db9b924485a441948", @@ -345,10 +345,10 @@ "reference": "mCherry", "target": "hND6", "blocking": "sample_number", + "method_differential": "deseq2", "fc_threshold": 1.5, "stat_threshold": 0.05, - "method_de": "deseq2", - "method": "gprofiler2" + "method_functional": "gprofiler2" }, [ "treatment_mCherry_hND6_sample_number_test.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,f55e010f72ee9200624137f42e94a5e5", @@ -379,7 +379,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-07T15:38:37.090983694" + "timestamp": "2025-02-13T10:44:00.530692637" }, "test gprofiler2 - mouse": { "content": [ @@ -391,7 +391,7 @@ "reference": "WT", "target": "KO", "blocking": "batch", - "method": "gprofiler2" + "method_functional": "gprofiler2" }, "Condition_genotype_WT_KO.gprofiler2.all_enriched_pathways.tsv:md5,31d1e4cfa1d09b30bf9126415cb93aff" ] @@ -404,7 +404,7 @@ "reference": "WT", "target": "KO", "blocking": "batch", - "method": "gprofiler2" + "method_functional": "gprofiler2" }, [ "Condition_genotype_WT_KO.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,6211f4fa1a226f3aaab77c3fb9318fe7", @@ -437,7 +437,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-07T15:36:34.167491274" + "timestamp": "2025-02-13T10:43:04.914828949" }, "deseq2 + gsea - mouse": { "content": [ @@ -449,8 +449,8 @@ "reference": "mCherry", "target": "hND6", "blocking": "", - "method_de": "deseq2", - "method": "gsea" + "method_differential": "deseq2", + "method_functional": "gsea" }, "treatment_mCherry_hND6__test.mh.all.v2022.1.Mm.symbols.gsea_report_for_mCherry.tsv:md5,ce8792382ae299749445767ff16aaecc", "treatment_mCherry_hND6__test.mh.all.v2022.1.Mm.symbols.gsea_report_for_hND6.tsv:md5,354a961c7e1417db2bf1f7e8d00c54f0" @@ -462,8 +462,8 @@ "reference": "mCherry", "target": "hND6", "blocking": "sample_number", - "method_de": "deseq2", - "method": "gsea" + "method_differential": "deseq2", + "method_functional": "gsea" }, "treatment_mCherry_hND6_sample_number_test.mh.all.v2022.1.Mm.symbols.gsea_report_for_mCherry.tsv:md5,ce8792382ae299749445767ff16aaecc", "treatment_mCherry_hND6_sample_number_test.mh.all.v2022.1.Mm.symbols.gsea_report_for_hND6.tsv:md5,354a961c7e1417db2bf1f7e8d00c54f0" @@ -488,7 +488,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-04T14:07:37.044833142" + "timestamp": "2025-02-13T11:17:37.142956026" }, "stub": { "content": [ @@ -501,7 +501,7 @@ "reference": "WT", "target": "KO", "blocking": "batch", - "method": "gprofiler2" + "method_functional": "gprofiler2" }, "Condition_genotype_WT_KO.gprofiler2.all_enriched_pathways.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -514,7 +514,7 @@ "reference": "WT", "target": "KO", "blocking": "batch", - "method": "gprofiler2" + "method_functional": "gprofiler2" }, "Condition_genotype_WT_KO.gprofiler2.*.sub_enriched_pathways.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -527,7 +527,7 @@ "reference": "WT", "target": "KO", "blocking": "batch", - "method": "gprofiler2" + "method_functional": "gprofiler2" }, "Condition_genotype_WT_KO.gprofiler2.gostplot.html:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -549,7 +549,7 @@ "reference": "WT", "target": "KO", "blocking": "batch", - "method": "gprofiler2" + "method_functional": "gprofiler2" }, "Condition_genotype_WT_KO.gprofiler2.all_enriched_pathways.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -562,7 +562,7 @@ "reference": "WT", "target": "KO", "blocking": "batch", - "method": "gprofiler2" + "method_functional": "gprofiler2" }, "Condition_genotype_WT_KO.gprofiler2.gostplot.html:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -575,7 +575,7 @@ "reference": "WT", "target": "KO", "blocking": "batch", - "method": "gprofiler2" + "method_functional": "gprofiler2" }, "Condition_genotype_WT_KO.gprofiler2.*.sub_enriched_pathways.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -592,9 +592,9 @@ } ], "meta": { - "nf-test": "0.9.1", - "nextflow": "24.10.3" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2025-01-24T17:38:14.74535" + "timestamp": "2025-02-13T10:46:46.236728565" } } \ No newline at end of file From ee7df96636f72673d0c0269de6394645759371c4 Mon Sep 17 00:00:00 2001 From: Suzanne Jin Date: Thu, 13 Feb 2025 11:36:03 +0000 Subject: [PATCH 15/15] fix: update version snapshots for the new propd container --- .../propr/propd/tests/main.nf.test.snap | 24 +++++++++---------- .../tests/main.nf.test.snap | 22 ++++++++--------- 2 files changed, 23 insertions(+), 23 deletions(-) diff --git a/modules/nf-core/propr/propd/tests/main.nf.test.snap b/modules/nf-core/propr/propd/tests/main.nf.test.snap index 318a5f0b7dd..e063f6b3c5d 100644 --- a/modules/nf-core/propr/propd/tests/main.nf.test.snap +++ b/modules/nf-core/propr/propd/tests/main.nf.test.snap @@ -14,15 +14,15 @@ ] ], [ - "versions.yml:md5,1d96e70c16cc53a1d7b2e1a54fd8b7e8" + "versions.yml:md5,f356eb5d430713b086255dfc32b5d6ee" ], "treatment_mCherry_hND6_.propd.genewise.png" ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nextflow": "24.10.4" }, - "timestamp": "2024-11-27T10:11:40.654796611" + "timestamp": "2025-02-13T11:28:17.523375516" }, "Test propr/propd when using Box-cox transformation": { "content": [ @@ -39,15 +39,15 @@ ] ], [ - "versions.yml:md5,1d96e70c16cc53a1d7b2e1a54fd8b7e8" + "versions.yml:md5,f356eb5d430713b086255dfc32b5d6ee" ], "treatment_mCherry_hND6_.propd.genewise.png" ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nextflow": "24.10.4" }, - "timestamp": "2024-11-27T10:12:22.252395938" + "timestamp": "2025-02-13T11:29:03.711287557" }, "Test propr/propd when using permutation tests": { "content": [ @@ -76,15 +76,15 @@ ] ], [ - "versions.yml:md5,1d96e70c16cc53a1d7b2e1a54fd8b7e8" + "versions.yml:md5,f356eb5d430713b086255dfc32b5d6ee" ], "treatment_mCherry_hND6_.propd.genewise.png" ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nextflow": "24.10.4" }, - "timestamp": "2024-11-27T10:13:03.55054778" + "timestamp": "2025-02-13T11:29:38.37807294" }, "Test propr/propd when saving all outputs": { "content": [ @@ -126,15 +126,15 @@ ], null, [ - "versions.yml:md5,1d96e70c16cc53a1d7b2e1a54fd8b7e8" + "versions.yml:md5,f356eb5d430713b086255dfc32b5d6ee" ], "treatment_mCherry_hND6_.propd.genewise.png", "treatment_mCherry_hND6_.propd.rds" ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nextflow": "24.10.4" }, - "timestamp": "2024-11-27T10:12:01.936451896" + "timestamp": "2025-02-13T11:28:45.957361627" } } \ No newline at end of file diff --git a/subworkflows/nf-core/abundance_differential_filter/tests/main.nf.test.snap b/subworkflows/nf-core/abundance_differential_filter/tests/main.nf.test.snap index ca7ba25f884..ace3db76d4f 100644 --- a/subworkflows/nf-core/abundance_differential_filter/tests/main.nf.test.snap +++ b/subworkflows/nf-core/abundance_differential_filter/tests/main.nf.test.snap @@ -28,7 +28,7 @@ ] ], [ - + ], [ [ @@ -564,17 +564,17 @@ [ "versions.yml:md5,1ddaab440e2528c688c05a02dd066f12", "versions.yml:md5,1ddaab440e2528c688c05a02dd066f12", + "versions.yml:md5,2a8f88e4b08dd4617efec4053ffa97f6", + "versions.yml:md5,2a8f88e4b08dd4617efec4053ffa97f6", "versions.yml:md5,2c0576aefff8da32c7c0cfd8529aa4b5", - "versions.yml:md5,2c0576aefff8da32c7c0cfd8529aa4b5", - "versions.yml:md5,da1c8ede6b02429770a53b2556e20622", - "versions.yml:md5,da1c8ede6b02429770a53b2556e20622" + "versions.yml:md5,2c0576aefff8da32c7c0cfd8529aa4b5" ] ], "meta": { "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-13T10:38:17.764737776" + "timestamp": "2025-02-13T11:32:15.319112521" }, "stub": { "content": [ @@ -632,7 +632,7 @@ ] ], "2": [ - + ], "3": [ [ @@ -683,7 +683,7 @@ "versions.yml:md5,05e3901f6d78f8839a7e07f422e9bc03" ], "adjacency": [ - + ], "model": [ [ @@ -1090,14 +1090,14 @@ ] ], [ - "versions.yml:md5,da1c8ede6b02429770a53b2556e20622", - "versions.yml:md5,da1c8ede6b02429770a53b2556e20622" + "versions.yml:md5,2a8f88e4b08dd4617efec4053ffa97f6", + "versions.yml:md5,2a8f88e4b08dd4617efec4053ffa97f6" ] ], "meta": { "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-13T10:35:58.616740674" + "timestamp": "2025-02-13T11:30:46.802705718" } -} +} \ No newline at end of file