diff --git a/bin/combine_tables.py b/bin/combine_tables.py index 46da929b..c4eaeb02 100755 --- a/bin/combine_tables.py +++ b/bin/combine_tables.py @@ -93,6 +93,8 @@ def main(args=None): results, gtdbtk_results, left_on="bin", right_on="user_genome", how="outer" ) # assuming depths for all bins are given + # sort results for reproducibility + results.sort_values(by='bin', inplace=True, ignore_index=True) results.to_csv(args.out, sep="\t") diff --git a/bin/summary_busco.py b/bin/summary_busco.py index b4a8c99b..faff6718 100755 --- a/bin/summary_busco.py +++ b/bin/summary_busco.py @@ -186,6 +186,8 @@ def main(args=None): else: df_final = df_specific.append(df_failed) + # sort output file for reproducibility + df_final.sort_values(by='GenomeBin', inplace=True) df_final.to_csv(args.out, sep="\t", index=False) diff --git a/conf/base.config b/conf/base.config index 714e0eb9..172df705 100644 --- a/conf/base.config +++ b/conf/base.config @@ -129,6 +129,13 @@ process { time = { check_max (16.h * task.attempt, 'time' ) } errorStrategy = { task.exitStatus in [143,137,104,134,139,250] ? 'retry' : 'finish' } } + //bowtie2 returns exit code 250 when running out of memory + withName: BOWTIE2_PHIX_REMOVAL_ALIGN { + cpus = { check_bowtie2_cpus (8, task.attempt ) } + memory = { check_max (40.GB * task.attempt, 'memory' ) } + time = { check_max (16.h * task.attempt, 'time' ) } + errorStrategy = { task.exitStatus in [143,137,104,134,139,250] ? 'retry' : 'finish' } + } //MEGAHIT returns exit code 250 when running out of memory withName: MEGAHIT { cpus = { check_megahit_cpus (8, task.attempt ) } diff --git a/conf/test.config b/conf/test.config index 4168c871..5968e844 100644 --- a/conf/test.config +++ b/conf/test.config @@ -24,14 +24,16 @@ params { centrifuge_db = "https://raw.githubusercontent.com/nf-core/test-datasets/mag/test_data/minigut_cf.tar.gz" kraken2_db = "https://raw.githubusercontent.com/nf-core/test-datasets/mag/test_data/minigut_kraken.tgz" skip_krona = true - min_length_unbinned_contigs = 1 + megahit_fix_cpu_1 = true + bowtie2_fix_cpu_1 = true + metabat2_fix_cpu_1 = true + maxbin2_fix_cpu_1 = true + concoct_fix_cpu_1 = true + binning_map_mode = 'own' + min_length_unbinned_contigs = 1000000 max_unbinned_contigs = 2 busco_db = "https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2020-03-06.tar.gz" busco_clean = true skip_gtdbtk = true skip_concoct = true - megahit_fix_cpu_1 = true - spades_fix_cpus = 2 - spadeshybrid_fix_cpus = 2 - metabat_rng_seed = 1 } diff --git a/conf/test_adapterremoval.config b/conf/test_adapterremoval.config index 54bb7959..07b02a6c 100644 --- a/conf/test_adapterremoval.config +++ b/conf/test_adapterremoval.config @@ -20,10 +20,9 @@ params { max_time = '6.h' // Input data - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/mag/samplesheets/samplesheet.multirun.csv' + input = 'https://raw.githubusercontent.com/nf-core/test-datasets/mag/samplesheets/samplesheet.euk.csv' clip_tool = 'adapterremoval' keep_phix = true - skip_adapter_trimming = true centrifuge_db = null kraken2_db = null skip_krona = true diff --git a/conf/test_ancient_dna.config b/conf/test_ancient_dna.config index 26752ad3..dcdda8fa 100644 --- a/conf/test_ancient_dna.config +++ b/conf/test_ancient_dna.config @@ -15,31 +15,37 @@ params { config_profile_description = 'Minimal test dataset to check pipeline function for ancient DNA step' // Limit resources so that this can run on GitHub Actions - //max_cpus = 2 - //max_memory = '6.GB' + max_cpus = 2 + max_memory = '6.GB' max_time = '6.h' // Input data - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/mag/samplesheets/samplesheet.csv' - skip_clipping = true - keep_phix = true - kraken2_db = null - centrifuge_db = null - skip_krona = true - megahit_fix_cpu_1 = true - skip_spades = false - spades_fix_cpus = 1 - skip_spadeshybrid = true - ancient_dna = true - skip_quast = true - skip_prodigal = true - bowtie2_fix_cpu_1 = true - binning_map_mode = 'own' - metabat2_fix_cpu_1 = true - maxbin2_fix_cpu_1 = true - concoct_fix_cpu_1 = true - skip_binqc = true - skip_gtdbtk = true - skip_prokka = true - skip_metaeuk = true + input = 'https://raw.githubusercontent.com/nf-core/test-datasets/mag/samplesheets/samplesheet.csv' + skip_clipping = true + keep_phix = true + kraken2_db = null + centrifuge_db = null + skip_krona = true + megahit_fix_cpu_1 = true + spades_fix_cpus = 1 + skip_spadeshybrid = true + ancient_dna = true + skip_quast = true + skip_prodigal = true + bowtie2_fix_cpu_1 = true + binning_map_mode = 'own' + metabat2_fix_cpu_1 = true + maxbin2_fix_cpu_1 = true + concoct_fix_cpu_1 = true + bcftools_view_high_variant_quality = 0 + bcftools_view_medium_variant_quality = 0 + bcftools_view_minimal_allelesupport = 3 + refine_bins_dastool = true + refine_bins_dastool_threshold = 0 + min_length_unbinned_contigs = 1 + max_unbinned_contigs = 2 + skip_binqc = true + skip_gtdbtk = true + skip_prokka = true + skip_metaeuk = true } diff --git a/conf/test_bbnorm.config b/conf/test_bbnorm.config index 8e7d6e94..c3fb8518 100644 --- a/conf/test_bbnorm.config +++ b/conf/test_bbnorm.config @@ -20,7 +20,7 @@ params { max_time = '6.h' // Input data - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/mag/samplesheets/samplesheet.multirun.csv' + input = 'https://raw.githubusercontent.com/nf-core/test-datasets/mag/samplesheets/samplesheet.csv' bbnorm = true keep_phix = true skip_adapter_trimming = true diff --git a/conf/test_binrefinement.config b/conf/test_binrefinement.config index bc1796d5..969dfc2c 100644 --- a/conf/test_binrefinement.config +++ b/conf/test_binrefinement.config @@ -20,18 +20,31 @@ params { max_time = '6.h' // Input data - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/mag/samplesheets/samplesheet.csv' - assembly_input = 'https://raw.githubusercontent.com/nf-core/test-datasets/mag/samplesheets/assembly_samplesheet.csv' - centrifuge_db = "https://raw.githubusercontent.com/nf-core/test-datasets/mag/test_data/minigut_cf.tar.gz" - kraken2_db = "https://raw.githubusercontent.com/nf-core/test-datasets/mag/test_data/minigut_kraken.tgz" - skip_krona = true - min_length_unbinned_contigs = 1 - max_unbinned_contigs = 2 - busco_db = "https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2020-03-06.tar.gz" - skip_gtdbtk = true - refine_bins_dastool = true - refine_bins_dastool_threshold = 0 - // TODO not using 'both' until #489 merged - postbinning_input = 'refined_bins_only' - busco_clean = true + input = 'https://raw.githubusercontent.com/nf-core/test-datasets/mag/samplesheets/samplesheet.csv' + assembly_input = 'https://raw.githubusercontent.com/nf-core/test-datasets/mag/samplesheets/assembly_samplesheet.csv' + bbnorm = true + keep_phix = true + skip_adapter_trimming = true + centrifuge_db = null + kraken2_db = null + skip_krona = true + skip_quast = true + skip_prodigal = true + bowtie2_fix_cpu_1 = true + metabat2_fix_cpu_1 = true + maxbin2_fix_cpu_1 = true + concoct_fix_cpu_1 = true + binning_map_mode = 'own' + min_length_unbinned_contigs = 1 + max_unbinned_contigs = 2 + refine_bins_dastool = true + refine_bins_dastool_threshold = 0 + // TODO not using 'both' until #489 merged + postbinning_input = 'refined_bins_only' + skip_busco = true + skip_binqc = true + skip_gtdbtk = true + skip_prokka = true + skip_metaeuk = true + } diff --git a/conf/test_busco_auto.config b/conf/test_busco_auto.config index 6479012f..d99ea24b 100644 --- a/conf/test_busco_auto.config +++ b/conf/test_busco_auto.config @@ -20,13 +20,26 @@ params { max_time = '6.h' // Input data - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/mag/samplesheets/samplesheet.csv' - skip_spades = true - min_length_unbinned_contigs = 1 - max_unbinned_contigs = 2 - skip_gtdbtk = true - skip_prokka = true - skip_prodigal = true - skip_quast = true - skip_concoct = true + input = 'https://raw.githubusercontent.com/nf-core/test-datasets/mag/samplesheets/samplesheet.csv' + keep_phix = true + skip_adapter_trimming = true + centrifuge_db = null + kraken2_db = null + skip_krona = true + megahit_fix_cpu_1 = true + skip_spades = true + skip_spadeshybrid = true + skip_quast = true + skip_prodigal = true + bowtie2_fix_cpu_1 = true + metabat2_fix_cpu_1 = true + maxbin2_fix_cpu_1 = true + concoct_fix_cpu_1 = true + binning_map_mode = 'own' + min_length_unbinned_contigs = 1 + max_unbinned_contigs = 2 + skip_concoct = true + skip_gtdbtk = true + skip_prokka = true + skip_metaeuk = true } diff --git a/conf/test_virus_identification.config b/conf/test_virus_identification.config index 635edb50..940f7e1d 100644 --- a/conf/test_virus_identification.config +++ b/conf/test_virus_identification.config @@ -21,10 +21,6 @@ params { // Input data input = 'https://raw.githubusercontent.com/nf-core/test-datasets/mag/samplesheets/samplesheet.multirun.csv' - run_virus_identification = true - genomad_splits = 7 - - // For computational efficiency keep_phix = true skip_clipping = true skip_adapter_trimming = true @@ -36,6 +32,8 @@ params { skip_spades = true skip_spadeshybrid = true skip_quast = true + run_virus_identification = true + genomad_splits = 7 skip_prodigal = true skip_binning = true skip_binqc = true diff --git a/subworkflows/local/busco_qc.nf b/subworkflows/local/busco_qc.nf index 15ab8cfa..f2686f62 100644 --- a/subworkflows/local/busco_qc.nf +++ b/subworkflows/local/busco_qc.nf @@ -76,7 +76,6 @@ workflow BUSCO_QC { ) emit: - summary_specific = BUSCO.out.summary_specific summary = BUSCO_SUMMARY.out.summary failed_bin = BUSCO.out.failed_bin.map{it[1]} multiqc = BUSCO.out.summary_domain.mix(BUSCO.out.summary_specific).map{it[1]} diff --git a/workflows/mag/main.nf b/workflows/mag/main.nf index 7ad1d9a5..880d41bf 100644 --- a/workflows/mag/main.nf +++ b/workflows/mag/main.nf @@ -225,10 +225,11 @@ if(params.metaeuk_db && !params.skip_metaeuk) { ch_binning_results_unbins = Channel.empty() ch_refined_bins = Channel.empty() ch_refined_unbins = Channel.empty() - ch_busco_summary_specific = Channel.empty() + ch_busco_summary = Channel.empty() ch_checkm_tsv = Channel.empty() ch_gunc_maxcss_level_tsv = Channel.empty() ch_quast_bin_summaries = Channel.empty() + ch_bin_summaries = Channel.empty() ch_cat_tax_classification_names = Channel.empty() ch_gtdbtk_summaries = Channel.empty() ch_prokka_faa = Channel.empty() @@ -881,7 +882,6 @@ workflow MAG { ch_input_bins_for_qc ) ch_busco_summary = BUSCO_QC.out.summary - ch_busco_summary_specific = BUSCO_QC.out.summary_specific ch_versions = ch_versions.mix(BUSCO_QC.out.versions.first()) // process information if BUSCO analysis failed for individual bins due to no matching genes BUSCO_QC.out @@ -1000,6 +1000,7 @@ workflow MAG { ch_quast_bins_summary.ifEmpty([]), ch_gtdbtk_summary.ifEmpty([]) ) + ch_bin_summaries = BIN_SUMMARY.out.summary } /* @@ -1120,39 +1121,13 @@ workflow MAG { emit: short_reads = ch_short_reads - // fastqc_raw = FASTQC_RAW.out.json - // adapterremoval_se = ADAPTERREMOVAL_SE.out.singles_truncated - // adapterremoval_pe = ADAPTERREMOVAL_PE.out.paired_truncated - // host_rm = BOWTIE2_HOST_REMOVAL_ALIGN.out.reads - // phix_rm = BOWTIE2_PHIX_REMOVAL_ALIGN.out.reads - // fastqc_trimmed = FASTQC_TRIMMED.out.json - // cat_fastq = CAT_FASTQ.out.reads - // seqtk = SEQTK_MERGEPE.out.reads - // bbmap = BBMAP_BBNORM.out.fastq - // nanoplot_raw = NANOPLOT_RAW.out.txt - // porechop = PORECHOP.out.reads - // nanolyse = NANOLYSE.out.reads - // filtlong = FILTLONG.out.reads - // nanoplot_filtered = NANOPLOT_FILTERED.out.txt - // kraken2 = KRAKEN2.out.report - // centrifuge = CENTRIFUGE.out.report assemblies = ch_assemblies - // megahit = ch_megahit_assemblies - // spades = ch_spades_assemblies - // spadeshybrid = ch_spadeshybrid_assemblies - // quast_contigs = QUAST.out.report prodigal = ch_prodigal_gene_annotations genomad = ch_genomad_virus_summary - bins = ch_binning_results_bins - unbins = ch_binning_results_unbins refined_bins = ch_refined_bins refined_unbins = ch_refined_unbins - busco = ch_busco_summary_specific - checkm = ch_checkm_tsv - gunc = ch_gunc_maxcss_level_tsv - quast_bins = ch_quast_bin_summaries + bin_summary = ch_bin_summaries cat = ch_cat_tax_classification_names - gtdbtk = ch_gtdbtk_summaries prokka = ch_prokka_faa metaeuk = ch_metaeuk_easypredict_faa versions = ch_versions diff --git a/workflows/mag/tests/main.nf.test b/workflows/mag/tests/main.nf.test new file mode 100644 index 00000000..b90b09b2 --- /dev/null +++ b/workflows/mag/tests/main.nf.test @@ -0,0 +1,21 @@ +nextflow_workflow { + + name "Test workflow: MAG" + script "../main.nf" + workflow "MAG" + tag "workflows" + tag "mag" + tag "mag_test" + + test("Default paramters") { + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out + ).match() } + ) + } + } +} diff --git a/workflows/mag/tests/main.nf.test.snap b/workflows/mag/tests/main.nf.test.snap new file mode 100644 index 00000000..1202ab2d --- /dev/null +++ b/workflows/mag/tests/main.nf.test.snap @@ -0,0 +1,543 @@ +{ + "Default paramters": { + "content": [ + { + "0": [ + [ + { + "id": "test_minigut", + "group": "0", + "single_end": false + }, + [ + "test_minigut_1.merged.fastq.gz:md5,fe81462f19e6acc0bbcec55528be7ad2", + "test_minigut_2.merged.fastq.gz:md5,88ebc2ac01082507f7be1761049e5eff" + ] + ], + [ + { + "id": "test_minigut_sample2", + "group": "0", + "single_end": false + }, + [ + 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"group": "0", "single_end": false }, [ - "test_minigut_1.merged.fastq.gz:md5,3ba44a474c09f2bc8770299fc6d327fb", - "test_minigut_2.merged.fastq.gz:md5,587c61c5f7bf3f0377f152ce9835bb88" + "test_minigut_euk_run0_ar2.pair1.truncated.fastq.gz:md5,e8f01a4fdf2e348330fc02a47eb3c5af", + "test_minigut_euk_run0_ar2.pair2.truncated.fastq.gz:md5,06510940505288d80a3d940db85d0ed5" ] ], [ { - "id": "test_minigut_sample2", + "id": "test_minigut_sample2_euk", "group": "0", "single_end": false }, [ - "test_minigut_sample2_run0_ar2.pair1.truncated.fastq.gz:md5,6ec5c5d6a273c2145096cd8a1488e159", - "test_minigut_sample2_run0_ar2.pair2.truncated.fastq.gz:md5,2c037d5d633998bf4b7006d30dc95610" + "test_minigut_sample2_euk_run0_ar2.pair1.truncated.fastq.gz:md5,92b8643e591f7490c980fe4d0879c955", + "test_minigut_sample2_euk_run0_ar2.pair2.truncated.fastq.gz:md5,7d4436e9532bb9665080b77efe441faf" ] ] ], @@ -30,26 +30,6 @@ ], "10": [ - - ], - "11": [ - - ], - "12": [ - - ], - "13": [ - - ], - "14": [ - - ], - "15": [ - - ], - "16": [ - "versions.yml:md5,3222fd64337a6c070682b63fc5e0cb3c", - "versions.yml:md5,9e5858bca5fb800545dc5c11f8503cc4", "versions.yml:md5,9e5858bca5fb800545dc5c11f8503cc4", "versions.yml:md5,9e5858bca5fb800545dc5c11f8503cc4", "versions.yml:md5,e9b46b38f7df41da088ff41127d3752a", @@ -82,26 +62,14 @@ "assemblies": [ ], - "bins": [ - - ], - "busco": [ + "bin_summary": [ ], "cat": [ - ], - "checkm": [ - ], "genomad": [ - ], - "gtdbtk": [ - - ], - "gunc": [ - ], "metaeuk": [ @@ -111,9 +79,6 @@ ], "prokka": [ - ], - "quast_bins": [ - ], "refined_bins": [ @@ -124,33 +89,28 @@ "short_reads": [ [ { - "id": "test_minigut", + "id": "test_minigut_euk", "group": "0", "single_end": false }, [ - "test_minigut_1.merged.fastq.gz:md5,3ba44a474c09f2bc8770299fc6d327fb", - "test_minigut_2.merged.fastq.gz:md5,587c61c5f7bf3f0377f152ce9835bb88" + "test_minigut_euk_run0_ar2.pair1.truncated.fastq.gz:md5,e8f01a4fdf2e348330fc02a47eb3c5af", + "test_minigut_euk_run0_ar2.pair2.truncated.fastq.gz:md5,06510940505288d80a3d940db85d0ed5" ] ], [ { - "id": "test_minigut_sample2", + "id": "test_minigut_sample2_euk", "group": "0", "single_end": false }, [ - "test_minigut_sample2_run0_ar2.pair1.truncated.fastq.gz:md5,6ec5c5d6a273c2145096cd8a1488e159", - "test_minigut_sample2_run0_ar2.pair2.truncated.fastq.gz:md5,2c037d5d633998bf4b7006d30dc95610" + "test_minigut_sample2_euk_run0_ar2.pair1.truncated.fastq.gz:md5,92b8643e591f7490c980fe4d0879c955", + "test_minigut_sample2_euk_run0_ar2.pair2.truncated.fastq.gz:md5,7d4436e9532bb9665080b77efe441faf" ] ] - ], - "unbins": [ - ], "versions": [ - "versions.yml:md5,3222fd64337a6c070682b63fc5e0cb3c", - "versions.yml:md5,9e5858bca5fb800545dc5c11f8503cc4", "versions.yml:md5,9e5858bca5fb800545dc5c11f8503cc4", "versions.yml:md5,9e5858bca5fb800545dc5c11f8503cc4", "versions.yml:md5,e9b46b38f7df41da088ff41127d3752a", @@ -158,6 +118,6 @@ ] } ], - "timestamp": "2023-12-14T11:34:38.395383683" + "timestamp": 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"2023-12-14T12:01:36.938067062" + "timestamp": "2024-01-02T13:06:14.895384486" } } \ No newline at end of file diff --git a/workflows/mag/tests/test_binrefinement.nf.test b/workflows/mag/tests/test_binrefinement.nf.test new file mode 100644 index 00000000..277b06e5 --- /dev/null +++ b/workflows/mag/tests/test_binrefinement.nf.test @@ -0,0 +1,21 @@ +nextflow_workflow { + + name "Test workflow: MAG" + script "../main.nf" + workflow "MAG" + tag "workflows" + tag "mag" + tag "mag_test_binrefinement" + + test("Parameters: refine_bins_dastool = true") { + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out + ).match() } + ) + } + } +} diff --git a/workflows/mag/tests/test_binrefinement.nf.test.snap b/workflows/mag/tests/test_binrefinement.nf.test.snap new file mode 100644 index 00000000..c4cc01c2 --- /dev/null +++ b/workflows/mag/tests/test_binrefinement.nf.test.snap @@ -0,0 +1,335 @@ +{ + "Parameters: refine_bins_dastool = true": { + "content": [ + { + 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"SPAdesHybrid-group-0_scaffolds.fasta:md5,84c68c6ba721ad5858588a1487e05b6f" ] ], - "bins": [ - - ], - "busco": [ + "bin_summary": [ ], "cat": [ - ], - "checkm": [ - ], "genomad": [ - ], - "gtdbtk": [ - - ], - "gunc": [ - ], "metaeuk": [ @@ -137,9 +107,6 @@ ], "prokka": [ - ], - "quast_bins": [ - ], "refined_bins": [ @@ -159,9 +126,6 @@ "minigut_run0_fastp_2.fastp.fastq.gz:md5,be6b3eb0d336c333e97d925b0e3a0ff6" ] ] - ], - "unbins": [ - ], "versions": [ "versions.yml:md5,15111ae1ae8b8b570a2efddd7c747bd0", @@ -176,6 +140,6 @@ ] } ], - "timestamp": "2023-12-14T14:09:37.526745496" + "timestamp": "2024-01-02T16:01:13.719391405" } } \ No newline at end of file diff --git a/workflows/mag/tests/test_hybrid_host_rm.nf.test.snap b/workflows/mag/tests/test_hybrid_host_rm.nf.test.snap index b4c23e10..3cb34ca8 100644 --- a/workflows/mag/tests/test_hybrid_host_rm.nf.test.snap +++ b/workflows/mag/tests/test_hybrid_host_rm.nf.test.snap @@ -27,24 +27,6 @@ ] ], "10": [ - - ], - "11": [ - - ], - "12": [ - - ], - "13": [ - - ], - "14": [ - - ], - "15": [ - - ], - "16": [ "versions.yml:md5,1bd6bbec156534880e04e0320dbce063", "versions.yml:md5,59050473c9f749b269ad7079fd4693df", "versions.yml:md5,5de8983775d3ef64cdbec6f382852619", @@ -89,26 +71,14 @@ "SPAdesHybrid-minigut_scaffolds.fasta:md5,d3c5e27f011a08daea597f9d2650436d" ] ], - "bins": [ - - ], - "busco": [ + "bin_summary": [ ], "cat": [ - ], - "checkm": [ - ], "genomad": [ - ], - "gtdbtk": [ - - ], - "gunc": [ - ], "metaeuk": [ @@ -118,9 +88,6 @@ ], "prokka": [ - ], - "quast_bins": [ - ], "refined_bins": [ @@ -140,9 +107,6 @@ "minigut_run0_host_removed.unmapped_2.fastq.gz:md5,b4246225aa4a15496991ac7c6b58563f" ] ] - ], - "unbins": [ - ], "versions": [ "versions.yml:md5,1bd6bbec156534880e04e0320dbce063", @@ -156,6 +120,6 @@ ] } ], - "timestamp": "2023-12-14T14:52:24.237611909" + "timestamp": "2024-01-02T15:43:00.831382408" } } \ No newline at end of file diff --git a/workflows/mag/tests/test_nothing.nf.test.snap b/workflows/mag/tests/test_nothing.nf.test.snap index a1a58ed6..ec39fd6a 100644 --- a/workflows/mag/tests/test_nothing.nf.test.snap +++ b/workflows/mag/tests/test_nothing.nf.test.snap @@ -30,24 +30,6 @@ ], "10": [ - - ], - "11": [ - - ], - "12": [ - - ], - "13": [ - - ], - "14": [ - - ], - "15": [ - - ], - "16": [ "versions.yml:md5,3222fd64337a6c070682b63fc5e0cb3c", "versions.yml:md5,e9b46b38f7df41da088ff41127d3752a" ], @@ -78,26 +60,14 @@ "assemblies": [ ], - "bins": [ - - ], - "busco": [ + "bin_summary": [ ], "cat": [ - ], - "checkm": [ - ], "genomad": [ - ], - "gtdbtk": [ - - ], - "gunc": [ - ], "metaeuk": [ @@ -107,9 +77,6 @@ ], "prokka": [ - ], - "quast_bins": [ - ], "refined_bins": [ @@ -140,9 +107,6 @@ "/nf-core/test-datasets/raw/mag/test_data/test_minigut_sample2_R2.fastq.gz" ] ] - ], - "unbins": [ - ], "versions": [ "versions.yml:md5,3222fd64337a6c070682b63fc5e0cb3c", @@ -150,6 +114,6 @@ ] } ], - "timestamp": "2023-12-14T11:38:30.168015353" + "timestamp": 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"metaeuk": [ @@ -140,9 +110,6 @@ ], "prokka": [ - ], - "quast_bins": [ - ], "refined_bins": [ @@ -173,9 +140,6 @@ "/nf-core/test-datasets/raw/mag/test_data/test_minigut_sample2_R2.fastq.gz" ] ] - ], - "unbins": [ - ], "versions": [ "versions.yml:md5,3222fd64337a6c070682b63fc5e0cb3c", @@ -184,6 +148,6 @@ ] } ], - "timestamp": "2023-12-14T11:48:19.010278472" + "timestamp": "2024-01-03T09:34:15.379927608" } } \ No newline at end of file