specified subworkflow:process name inside modules.config

nf-core · Oct 22, 2024 · f08aa0b · f08aa0b
1 parent 7560a55
commit f08aa0b
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Showing 3 changed files with 6 additions and 5 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -321,7 +321,7 @@ process {
         ].join(' ').trim() }
     }
 
-    withName: GPROFILER2_GOST {
+    withName: 'NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GPROFILER2_GOST' {
         publishDir = [
             [
                 path: { "${params.outdir}/tables/gprofiler2/${meta.id}/" },
@@ -581,8 +581,7 @@ process {
         ]
     }
 
-    // TODO name this based on the subworkflow:process
-    withName: GPROFILER2_GOST_EXPERIMENTAL {
+    withName: 'NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:EXPERIMENTAL:ENRICHMENT:GPROFILER2_GOST' {
         tag = { [
             "$meta.id",
             (meta.contrast ? "$meta.contrast" : ''),

diff --git a/subworkflows/local/enrichment/main.nf b/subworkflows/local/enrichment/main.nf
@@ -3,7 +3,7 @@
 //
 include { MYGENE } from "../../../modules/nf-core/mygene/main.nf"
 include { PROPR_GREA as GREA } from "../../../modules/local/propr/grea/main.nf"
-include { GPROFILER2_GOST as GPROFILER2_GOST_EXPERIMENTAL } from "../../../modules/nf-core/gprofiler2/gost/main.nf"
+include { GPROFILER2_GOST } from "../../../modules/nf-core/gprofiler2/gost/main.nf"
 
 workflow ENRICHMENT {
     take:
@@ -70,7 +70,7 @@ workflow ENRICHMENT {
         }
         .set{ ch_enrichment_gprofiler2 }
 
-    GPROFILER2_GOST_EXPERIMENTAL(
+    GPROFILER2_GOST(
         ch_enrichment_gprofiler2.de,
         ch_enrichment_gprofiler2.gmt,
         ch_enrichment_gprofiler2.background

diff --git a/workflows/differentialabundance.nf b/workflows/differentialabundance.nf
@@ -359,6 +359,8 @@ workflow DIFFERENTIALABUNDANCE {
         ch_processed_matrices = ch_norm
             .map{ it.tail() }
             .first()
+
+    // TODO the experimental branch should be independent from this file
     } else if (params.study_type == 'experimental') {
 
         // Convert the samplesheet.csv in a channel with the proper format