change to workDir

nf-core · Apr 10, 2024 · 03e9e82 · 03e9e82
1 parent a92e697
commit 03e9e82
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/subworkflows/local/align_cellrangermulti.nf b/subworkflows/local/align_cellrangermulti.nf
@@ -96,7 +96,7 @@ workflow CELLRANGER_MULTI_ALIGN {
                 if (meta && meta[0][0].containsKey('cmo_ids')) {
                     lines = [ 'sample_id,cmo_ids,description' ]
                     meta[0].each{ lines = lines + [ "$it.multiplexed_sample_id,$it.cmo_ids,$it.description" ] }
-                    cmos = file( "${sample}_cmo_samplesheet.csv" )
+                    cmos = file( "${workflow.workDir}/${sample}_cmo_samplesheet.csv" )
                     cmos.text = lines.join("\n").trim().toString()
                     cmos
                 } else { empty_file }
@@ -111,7 +111,7 @@ workflow CELLRANGER_MULTI_ALIGN {
                 if (meta && meta[0][0].containsKey('probe_barcode_ids')) {
                     lines = [ 'sample_id,probe_barcode_ids,description' ]
                     meta[0].each{ lines = lines + [ "$it.multiplexed_sample_id,$it.probe_barcode_ids,$it.description" ] }
-                    frna = file( "${sample}_frna_samplesheet.csv" )
+                    frna = file( "${workflow.workDir}/${sample}_frna_samplesheet.csv" )
                     frna.text = lines.join("\n").trim().toString()
                     frna
                 } else { empty_file }