Add patch to multiqc module so that it can now accept a meta map as i…

…nput
mskcc · May 18, 2023 · 8f3550d · 8f3550d
1 parent d26bcff
commit 8f3550d
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Showing 7 changed files with 52 additions and 7 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -35,7 +35,7 @@ process {
         ]
     }
 
-    withName: '.*:QC:MULTIQC' {
+    withName: '.*:QC:MULTIQC_COLLECT' {
         publishDir = [
             path: { "${params.outdir}/multiqc" },
             mode: params.publish_dir_mode,

diff --git a/modules.json b/modules.json
@@ -48,7 +48,8 @@
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "ee80d14721e76e2e079103b8dcd5d57129e584ba",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/multiqc/multiqc.diff"
                     },
                     "picard/collecthsmetrics": {
                         "branch": "master",

diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml
diff --git a/modules/nf-core/multiqc/multiqc.diff b/modules/nf-core/multiqc/multiqc.diff
diff --git a/subworkflows/local/qc.nf b/subworkflows/local/qc.nf
@@ -2,7 +2,10 @@ ch_multiqc_config          = Channel.fromPath("$projectDir/assets/multiqc_config
 
 include { PICARD_COLLECTRNASEQMETRICS } from '../../modules/nf-core/picard/collectrnaseqmetrics/main'
 include { PICARD_COLLECTHSMETRICS     } from '../../modules/nf-core/picard/collecthsmetrics/main'
-include { MULTIQC                     } from '../../modules/nf-core/multiqc/main'
+include {
+    MULTIQC ;
+    MULTIQC as MULTIQC_COLLECT
+} from '../../modules/nf-core/multiqc/main'
 
 workflow QC {
 
@@ -47,8 +50,6 @@ workflow QC {
     multiqc_ch = PICARD_COLLECTRNASEQMETRICS.out.metrics
         .mix(fastp_json)
         .mix(PICARD_COLLECTHSMETRICS.out.metrics)
-        .map{meta, multiqc_files -> multiqc_files }
-        .collect()
 
     MULTIQC(
         multiqc_ch,
@@ -57,6 +58,13 @@ workflow QC {
         []
     )
 
+    MULTIQC_COLLECT(
+        multiqc_ch.map{meta, multiqc_files -> multiqc_files}.collect().map{[[:],it]},
+        ch_multiqc_config.collect().ifEmpty([]),
+        [],
+        []
+    )
+
     emit:
     ch_versions
 

diff --git a/workflows/forte.nf b/workflows/forte.nf
@@ -153,7 +153,7 @@ workflow FORTE {
     ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml'))
     ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
 
-    ch_multiqc_files.collect()
+    ch_multiqc_files.collect().map{ files -> [[:], files] }
 
     MULTIQC (
         ch_multiqc_files.collect(),