Merge pull request #88 from LouisLeNezet/multiqc

Multiqc
nf-core · Jun 17, 2024 · 20956e6 · 20956e6
2 parents 150cb9e + 8964fe2
commit 20956e6
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Showing 39 changed files with 1,013 additions and 343 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -33,6 +33,7 @@ Initial release of nf-core/phaseimpute, created with the [nf-core](https://nf-co
 - [#84](https://github.com/nf-core/phaseimpute/pull/84) - Change depth computation to use SAMTOOLS_DEPTH and make separation by chromosome only if regions are specified.
 - [#85](https://github.com/nf-core/phaseimpute/pull/85) - Use external params in individual tests for tools.
 - [#86](https://github.com/nf-core/phaseimpute/pull/86) - Move `bcftools_convert` to `vcf_sites_extract_bcftools`.
+- [#88](https://github.com/nf-core/phaseimpute/pull/88) - Improve multiqc report with more information.
 
 ### `Fixed`
 

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -10,6 +10,10 @@ report_section_order:
   "nf-core-phaseimpute-summary":
     order: -1002
 
+top_modules:
+  - samtools
+  - bcftools
+
 export_plots: true
 
 disable_version_detection: true
diff --git a/assets/schema_input.json b/assets/schema_input.json
@@ -9,8 +9,8 @@
         "properties": {
             "sample": {
                 "type": "string",
-                "pattern": "^\\S+$",
-                "errorMessage": "Sample name must be provided and cannot contain spaces",
+                "pattern": "^[a-zA-Z0-9_]+$",
+                "errorMessage": "Sample name must be provided and cannot contain spaces nor special character '.' .",
                 "meta": ["id"]
             },
             "file": {

diff --git a/conf/modules.config b/conf/modules.config
@@ -18,12 +18,57 @@ process {
         saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
     ]
 
-    withName: 'MULTIQC' {
+    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:MULTIQC' {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
         publishDir = [
             path: { "${params.outdir}/multiqc" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
+
+    // Stats
+    // Simulation
+    // Coverage process
+    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:SAMTOOLS_COVERAGE_TRT' {
+        ext.prefix = { "${meta.id}.A-truth" }
+        publishDir = [ enabled: false ]
+    }
+    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:SAMTOOLS_COVERAGE_SIM' {
+        ext.prefix = { "${meta.id}.B-sim" }
+        publishDir = [ enabled: false ]
+    }
+
+    // VCF
+    // PANEL
+    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BCFTOOLS_STATS_PANEL' {
+        ext.prefix = { "${meta.id}.panel" }
+        publishDir = [
+            path: { "${params.outdir}/prep_panel/stats/" },
+            mode: params.publish_dir_mode,
+            enabled: true,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    // TRUTH
+    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BCFTOOLS_STATS_TRUTH' {
+        ext.prefix = { "${meta.id}.truth" }
+        publishDir = [
+            path: { "${params.outdir}/validation/stats" },
+            mode: params.publish_dir_mode,
+            enabled: true,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+    // IMPUTE
+    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BCFTOOLS_STATS_TOOLS' {
+        ext.prefix = { "${meta.id}.${meta.tools}" }
+        publishDir = [
+            path: { "${params.outdir}/imputation/stats" },
+            mode: params.publish_dir_mode,
+            enabled: true,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
 }
diff --git a/conf/steps/imputation_glimpse1.config b/conf/steps/imputation_glimpse1.config
@@ -34,7 +34,7 @@ process {
             "-Aim",
             "-C alleles"
         ].join(' ')
-        ext.prefix = { "${meta.id}.call" }
+        ext.prefix = { "${meta.id}" }
     }
 
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_IMPUTE_GLIMPSE1:BAM_GL_BCFTOOLS:BCFTOOLS_ANNOTATE' {
@@ -74,16 +74,16 @@ process {
         publishDir = [
             path: { "${params.outdir}/imputation/glimpse1/concat" },
             mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_GLIMPSE1:BCFTOOLS_CONCAT' {
         ext.args   = ["--ligate", "--output-type z"].join(' ')
-        ext.prefix = { "${meta.id}_glimpse1" }
+        ext.prefix = { "${meta.id}.glimpse1" }
     }
 
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_GLIMPSE1:BCFTOOLS_INDEX' {
         ext.args     = "--tbi"
-        ext.prefix = { "${meta.id}_glimpse1" }
     }
 }
diff --git a/conf/steps/imputation_glimpse2.config b/conf/steps/imputation_glimpse2.config
@@ -20,12 +20,12 @@ process {
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_IMPUTE_GLIMPSE2:GLIMPSE2_PHASE' {
         ext.prefix   = { "${meta.id}_${meta.chunk.replace(':','_')}_glimpse2" }
         ext.args     = "--keep-monomorphic-ref-sites"
-        ext.suffix   = "vcf.gz"
+        ext.suffix   = "bcf"
         publishDir   = [ enabled: false ]
     }
 
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_IMPUTE_GLIMPSE2:BCFTOOLS_INDEX_1' {
-        ext.args     = "--tbi"
+        ext.args     = "--csi"
         publishDir   = [ enabled: false ]
     }
 
@@ -45,17 +45,17 @@ process {
         publishDir = [
             path: { "${params.outdir}/imputation/glimpse2/concat" },
             mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_GLIMPSE2:BCFTOOLS_CONCAT' {
         ext.args   = ["--ligate", "--output-type z"].join(' ')
-        ext.prefix = { "${meta.id}_glimpse2" }
+        ext.prefix = { "${meta.id}.glimpse2" }
     }
 
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_GLIMPSE2:BCFTOOLS_INDEX' {
         ext.args     = "--tbi"
-        ext.prefix = { "${meta.id}_glimpse2" }
     }
 
 }
diff --git a/conf/steps/imputation_quilt.config b/conf/steps/imputation_quilt.config
@@ -48,17 +48,17 @@ process {
         publishDir = [
             path: { "${params.outdir}/imputation/quilt/concat" },
             mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_QUILT:BCFTOOLS_CONCAT' {
         ext.args = ["--ligate", "--output-type z",].join(' ')
-        ext.prefix = { "${meta.id}_quilt" }
+        ext.prefix = { "${meta.id}.quilt" }
     }
 
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_QUILT:BCFTOOLS_INDEX' {
         ext.args     = "--tbi"
-        ext.prefix = { "${meta.id}_quilt" }
     }
 
 }
diff --git a/conf/steps/imputation_stitch.config b/conf/steps/imputation_stitch.config
@@ -30,7 +30,7 @@ process {
     }
 
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_IMPUTE_STITCH:STITCH' {
-        ext.prefix = { "${meta.id}_stitch" }
+        ext.prefix = { "${meta.id}.stitch" }
     }
 
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_IMPUTE_STITCH:BCFTOOLS_INDEX' {
@@ -44,23 +44,23 @@ process {
 
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_STITCH:BCFTOOLS_CONCAT' {
         ext.args   = ["--ligate", "--output-type z"].join(' ')
-        ext.prefix = { "${meta.id}_stitch" }
     }
 
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_STITCH:BCFTOOLS_INDEX' {
         ext.args   = "--tbi"
-        ext.prefix = { "${meta.id}_stitch" }
     }
 
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_SAMPLES_BCFTOOLS:.*' {
         publishDir = [
             path: { "${params.outdir}/imputation/stitch/concat" },
             mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_SAMPLES_BCFTOOLS:BCFTOOLS_PLUGINSPLIT' {
         ext.args   = "-Oz"
+        ext.suffix = ".stitch"
     }
 
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_SAMPLES_BCFTOOLS:BCFTOOLS_INDEX' {

diff --git a/conf/steps/panel_prep.config b/conf/steps/panel_prep.config
@@ -15,6 +15,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/prep_panel/" },
             mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
             enabled: false
         ]
         tag = {"${meta.id} ${meta.chr}"}
@@ -55,6 +56,7 @@ process {
         ext.prefix    = { "${meta.id}_${meta.chr}_biallelic_snps" }
         publishDir = [
             path: { "${params.outdir}/prep_panel/normalized" },
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
             enabled: true
         ]
         }
@@ -63,6 +65,7 @@ process {
         ext.args     = "--tbi"
         publishDir = [
             path: { "${params.outdir}/prep_panel/normalized" },
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
             enabled: true
         ]
         }
@@ -73,6 +76,7 @@ process {
         ext.prefix    = { "${meta.id}_${meta.chr}_biallelic_removed_samples" }
         publishDir = [
             path: { "${params.outdir}/prep_panel/normalized" },
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
             enabled: true
         ]
     }
@@ -81,6 +85,7 @@ process {
         ext.args     = "--tbi"
         publishDir = [
             path: { "${params.outdir}/prep_panel/normalized" },
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
             enabled: true
         ]
     }
@@ -89,6 +94,7 @@ process {
         ext.prefix   = { "${meta.id}_${meta.chr}" }
         publishDir = [
             path: { "${params.outdir}/prep_panel/compute_freq" },
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
             enabled: true
         ]
     }
@@ -106,6 +112,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/prep_panel/phasing" },
             mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
             enabled: false
         ]
         tag = {"${meta.id} ${meta.chr}"}
@@ -131,6 +138,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/prep_panel/haplegend/" },
             mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
             enabled: true
         ]
     }
@@ -148,6 +156,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/prep_panel/sites/vcf/" },
             mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
             enabled: true
         ]
     }
@@ -157,6 +166,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/prep_panel/sites/vcf/" },
             mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
             enabled: true
         ]
     }
@@ -171,13 +181,20 @@ process {
         ext.args   = "'{ gsub(\",\", \"\\t\") ; key = \$1 FS \$2 } !seen[key]++'" // Remove duplicates
         ext.prefix = { "${meta.id}_${meta.chr}_posfile_stitch" }
         ext.suffix = "txt"
+        publishDir = [
+            path: { "${params.outdir}/prep_panel/posfile/" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+            enabled: true
+        ]
     }
 
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_SITES_EXTRACT_BCFTOOLS:TABIX_BGZIP' {
         ext.prefix = { "${meta.id}_${meta.chr}_glimpse1_sites_tsv" }
         publishDir = [
             path: { "${params.outdir}/prep_panel/sites/tsv/" },
             mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
             enabled: true
         ]
     }
@@ -192,6 +209,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/prep_panel/sites/tsv/" },
             mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
             enabled: true
         ]
     }
@@ -201,6 +219,10 @@ process {
         publishDir = [ enabled: false ]
     }
 
+    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_PANEL:BCFTOOLS_CONCAT' {
+        ext.prefix = { "${meta.id}.panel" }
+    }
+
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_PANEL:BCFTOOLS_INDEX' {
         ext.args = "--tbi"
     }
@@ -210,6 +232,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/prep_panel/chunks/" },
             mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
             enabled: true
         ]
         tag = {"${meta.id} ${meta.chr}"}
@@ -220,6 +243,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/prep_panel/chunks/glimpse1/" },
             mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
             enabled: true
         ]
     }
@@ -229,6 +253,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/prep_panel/chunks/glimpse2/" },
             mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
             enabled: true
         ]
     }
@@ -238,6 +263,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/prep_panel/chunks/glimpse2/" },
             mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
             enabled: true
         ]
     }

diff --git a/conf/steps/simulation.config b/conf/steps/simulation.config
@@ -57,14 +57,4 @@ process {
         ext.args = ""
         tag = {"${meta.id}"}
     }
-
-    // Coverage process
-    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:SAMTOOLS_COVERAGE_TRT' {
-        ext.prefix = { "${meta.id}_truth" }
-        publishDir = [ enabled: false ]
-    }
-    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:SAMTOOLS_COVERAGE_SIM' {
-        ext.prefix = { "${meta.id}" }
-        publishDir = [ enabled: false ]
-    }
 }
diff --git a/conf/steps/validation.config b/conf/steps/validation.config
@@ -29,7 +29,7 @@ process {
             "-Aim",
             "-C alleles"
         ].join(' ')
-        ext.prefix = { "${meta.id}_truth.call" }
+        ext.prefix = { "${meta.id}_truth" }
     }
 
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:GL_TRUTH:BCFTOOLS_ANNOTATE' {
@@ -43,7 +43,6 @@ process {
 
     // Concatenate the truth set
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_TRUTH:.*' {
-        ext.prefix = { "${meta.id}_truth_concat" }
         publishDir = [
             path: { "${params.outdir}/validation/concat" },
             mode: params.publish_dir_mode,
@@ -53,6 +52,7 @@ process {
 
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_TRUTH:BCFTOOLS_CONCAT' {
         ext.args = ["--ligate", "--output-type z",].join(' ')
+        ext.prefix = { "${meta.id}.A-truth" }
     }
 
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_TRUTH:BCFTOOLS_INDEX' {