fix channel i/o

nf-core · Aug 28, 2023 · 1160d70 · 1160d70
1 parent cfec479
commit 1160d70
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/subworkflows/local/qc_workflow.nf b/subworkflows/local/qc_workflow.nf
@@ -18,15 +18,15 @@ workflow QC_WORKFLOW {
     main:
         ch_versions = Channel.empty()
 
-        QUALIMAP_RNASEQ(bam_sorted, ch_chrgtf)
+        QUALIMAP_RNASEQ(ch_bam_sorted_indexed, ch_chrgtf)
         ch_versions = ch_versions.mix(QUALIMAP_RNASEQ.out.versions)
         ch_qualimap_qc = Channel.empty().mix(QUALIMAP_RNASEQ.out.results)
 
         PICARD_COLLECTRNASEQMETRICS(ch_bam_sorted_indexed, ch_refflat, ch_rrna_interval)
         ch_versions = ch_versions.mix(PICARD_COLLECTRNASEQMETRICS.out.versions)
         ch_rnaseq_metrics = Channel.empty().mix(PICARD_COLLECTRNASEQMETRICS.out.metrics)
 
-        PICARD_MARKDUPLICATES(bam_sorted, ch_fasta, ch_fai)
+        PICARD_MARKDUPLICATES(ch_bam_sorted_indexed, ch_fasta, ch_fai)
         ch_versions = ch_versions.mix(PICARD_MARKDUPLICATES.out.versions)
         ch_duplicate_metrics = Channel.empty().mix(PICARD_MARKDUPLICATES.out.metrics)