Merge pull request #1352 from nf-core/harmonize_new_for_multiqc

pinin4fjords · web-flow · commit cb53ef32dfad · 2024-08-20T10:53:56.000+01:00
Assorted fixes to MultiQC usage
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -109,6 +109,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #1345](https://github.com/nf-core/rnaseq/pull/1345) - Fix preprocessing call
 - [PR #1350](https://github.com/nf-core/rnaseq/pull/1350) - Reduce resource usage for sort process in bedtools/genomecov
 - [PR #1353](https://github.com/nf-core/rnaseq/pull/1353) - Correct conditional for salmon indexing in preprocessing workflow
+- [PR #1352](https://github.com/nf-core/rnaseq/pull/1352) - Assorted fixes to MultiQC usage
 - [PR #1355](https://github.com/nf-core/rnaseq/pull/1355) - Make all curves on subway map better looking, and all lines now have the same width
 
 ### Parameters
diff --git a/modules.json b/modules.json
@@ -92,7 +92,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "b80f5fd12ff7c43938f424dd76392a2704fa2396",
+                        "git_sha": "878d2adbb911aa6e15c06a4d1e93d01bd6f26c74",
                         "installed_by": ["modules"]
                     },
                     "picard/markduplicates": {
@@ -324,7 +324,7 @@
                     },
                     "fastq_qc_trim_filter_setstrandedness": {
                         "branch": "master",
-                        "git_sha": "22c8d535286728605ccd229e5d1bb014cb965f8f",
+                        "git_sha": "8c47be6a114b82a6e6d2f5320b3b5c67579956c0",
                         "installed_by": ["subworkflows"]
                     },
                     "fastq_subsample_fq_salmon": {
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
diff --git a/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf b/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf
@@ -493,18 +493,6 @@ def checkMaxContigSize(fai_file) {
     }
 }
 
-//
-// Create MultiQC tsv custom content from a list of values
-//
-def multiqcTsvFromList(tsv_data, header) {
-    def tsv_string = ""
-    if (tsv_data.size() > 0) {
-        tsv_string += "${header.join('\t')}\n"
-        tsv_string += tsv_data.join('\n')
-    }
-    return tsv_string
-}
-
 //
 // Function that parses and returns the alignment rate from the STAR log output
 //
diff --git a/subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.function.nf.test b/subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.function.nf.test
@@ -367,29 +367,6 @@ nextflow_function {
     }
 
 
-    test("Test Function multiqcTsvFromList") {
-
-        function "multiqcTsvFromList"
-
-        when {
-            function {
-                """
-                // Create a TSV of one entry
-                input[0] = [ 'test', 'value'    ]
-                input[1] = [ 'id'  , 'attribute']
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert function.success },
-                { assert snapshot(function.result).match() }
-            )
-        }
-
-    }
-
     test("Test Function getStarPercentMapped pass") {
 
         function "getStarPercentMapped"
diff --git a/subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.function.nf.test.snap b/subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.function.nf.test.snap
@@ -95,16 +95,6 @@
         },
         "timestamp": "2024-03-06T14:33:40.548126"
     },
-    "Test Function multiqcTsvFromList": {
-        "content": [
-            "id\tattribute\ntest\nvalue"
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-03-06T14:33:43.671826"
-    },
     "Test Function checkSamplesAfterGrouping success": {
         "content": [
             [
diff --git a/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf b/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf
diff --git a/tests/nextflow.config b/tests/nextflow.config
@@ -27,6 +27,9 @@ process {
         memory = 3.GB
         time   = 2.h
     }
+    withName: 'MULTIQC' {
+        ext.prefix = null
+    }
 }
 
 // Impose same minimum Nextflow version as the pipeline for testing
diff --git a/workflows/rnaseq/assets/multiqc/deseq2_clustering_header.txt b/workflows/rnaseq/assets/multiqc/deseq2_clustering_header.txt
@@ -4,6 +4,9 @@
 #	       <a href='https://bioconductor.org/packages/release/bioc/html/DESeq2.html' target='_blank'>DESeq2</a>
 #              rlog values for each sample
 #              in the <a href='https://github.com/nf-core/rnaseq/blob/master/bin/deseq2_qc.r'><code>deseq2_qc.r</code></a> script."
+#parent_id: 'sample-relationships'
+#parent_name: 'Sample relationships'
+#parent_description: 'Plots interrogating sample relationships, based on final count matrices'
 #plot_type: 'heatmap'
 #anchor: 'deseq2_clustering'
 #pconfig:
diff --git a/workflows/rnaseq/assets/multiqc/deseq2_pca_header.txt b/workflows/rnaseq/assets/multiqc/deseq2_pca_header.txt
@@ -3,6 +3,9 @@
 #description: "PCA plot between samples in the experiment.
 #              These values are calculated using <a href='https://bioconductor.org/packages/release/bioc/html/DESeq2.html'>DESeq2</a>
 #              in the <a href='https://github.com/nf-core/rnaseq/blob/master/bin/deseq2_qc.r'><code>deseq2_qc.r</code></a> script."
+#parent_id: 'sample-relationships'
+#parent_name: 'Sample relationships'
+#parent_description: 'Plots interrogating sample relationships, based on final count matrices'
 #plot_type: 'scatter'
 #anchor: 'deseq2_pca'
 #pconfig:
diff --git a/workflows/rnaseq/assets/multiqc/multiqc_config.yml b/workflows/rnaseq/assets/multiqc/multiqc_config.yml
@@ -1,6 +1,69 @@
 report_comment: >
   This report has been generated by the <a href="https://github.com/nf-core/rnaseq/tree/dev" target="_blank">nf-core/rnaseq</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/rnaseq/dev/docs/output" target="_blank">documentation</a>.
 report_section_order:
+  # Important checks and failures
+  sample-status:
+    order: 5004
+  fail_trimmed_samples-module:
+    order: 5003
+  fail_mapped_samples-module:
+    order: 5002
+  fail_strand_check-module:
+    order: 5001
+  # Preprocessing and pre-alignment QC
+  fastqc_raw:
+    order: 4004
+  cutadapt:
+    order: 4003
+  fastp:
+    order: 4003
+  fastqc_trimmed:
+    order: 4002
+  # Alignment
+  star:
+    order: 3000
+  hisat2:
+    order: 3000
+  # Post-alignment QC
+  samtools:
+    order: 3000
+  dupradar-module:
+    order: 3000
+  featurecounts_biotype:
+    order: 3000
+  picard:
+    order: 3000
+  preseq:
+    order: 3000
+  qualimap:
+    order: 3000
+  rseqc:
+    order: 3000
+  umitools:
+    order: 3000
+  # Quantification
+  rsem:
+    order: 2000
+  salmon:
+    order: 2000
+  kallisto:
+    order: 2000
+  # Post-quantification QC
+  sample-relationships:
+    order: 1006
+  star_salmon_deseq2_pca:
+    order: 1005
+  star_salmon_deseq2_clustering:
+    order: 1004
+  salmon_deseq2_pca:
+    order: 1003
+  salmon_deseq2_clustering:
+    order: 1002
+  star_rsem_deseq2_pca:
+    order: 1001
+  star_rsem_deseq2_clustering:
+    order: 1000
+  # Summaries
   "nf-core-rnaseq-methods-description-module":
     order: -1000
   "software_versions-module":
@@ -32,18 +95,6 @@ run_modules:
   - qualimap
 
 # Order of modules
-top_modules:
-  - "fail_trimmed_samples"
-  - "fail_mapped_samples"
-  - "fail_strand_check"
-  - "star_rsem_deseq2_pca"
-  - "star_rsem_deseq2_clustering"
-  - "star_salmon_deseq2_pca"
-  - "star_salmon_deseq2_clustering"
-  - "salmon_deseq2_pca"
-  - "salmon_deseq2_clustering"
-  - "biotype_counts"
-  - "dupradar"
 
 module_order:
   - fastqc:
diff --git a/workflows/rnaseq/assets/multiqc/sample_status_header.txt b/workflows/rnaseq/assets/multiqc/sample_status_header.txt
@@ -0,0 +1,3 @@
+#parent_id: 'sample-status'
+#parent_name: 'Sample status checks'
+#parent_description: 'Reports on sample strandedness status, and any failures in trimming or mapping'
diff --git a/workflows/rnaseq/main.nf b/workflows/rnaseq/main.nf

Original file line number	Diff line number	Diff line change
`@@ -27,6 +27,9 @@ process {`
`27`	`27`	`memory = 3.GB`
`28`	`28`	`time = 2.h`
`29`	`29`	`}`
	`30`	`+ withName: 'MULTIQC' {`
	`31`	`+ ext.prefix = null`
	`32`	`+ }`
`30`	`33`	`}`
`31`	`34`
`32`	`35`	`// Impose same minimum Nextflow version as the pipeline for testing`