Merge pull request #4 from charles-plessy/target__query

Fix file names in QC modules
nf-core · Jun 19, 2024 · b5862bd · b5862bd
2 parents 9a4724f + ae22d57
commit b5862bd
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Showing 2 changed files with 5 additions and 4 deletions.
diff --git a/main.nf b/main.nf
@@ -91,14 +91,11 @@ workflow {
         .map { file_obj -> [ [id:params.targetName], file_obj] }
         .set { ch_target }
 
-    ch_query = PIPELINE_INITIALISATION.out.samplesheet
-        .map { row -> [ [id: params.targetName + '___' + row[0].id] , row.tail() ] }
-
     //
     // WORKFLOW: Run main workflow
     //
     NFCORE_PAIRGENOMEALIGN (
-        ch_query,
+        PIPELINE_INITIALISATION.out.samplesheet,
         ch_target
     )
 

diff --git a/workflows/pairgenomealign.nf b/workflows/pairgenomealign.nf
@@ -55,6 +55,10 @@ workflow PAIRGENOMEALIGN {
     ch_multiqc_files = ch_multiqc_files.mix(ASSEMBLYSCAN.out.json.collect{it[1]})
     ch_versions = ch_versions.mix(ASSEMBLYSCAN.out.versions.first())
 
+    // Prefix id with target genome name before producing alignment files
+    ch_samplesheet = ch_samplesheet
+        .map { row -> [ [id: params.targetName + '___' + row[0].id] , row.tail() ] }
+
     //
     // SUBWORKFLOW: pairalign_m2o
     //