fix samtools/sort usage

maxulysse · Mar 8, 2024 · 12f0441 · 12f0441
1 parent c827f74
commit 12f0441
Showing 1 changed file with 2 additions and 1 deletion.
diff --git a/workflows/rnaseq/main.nf b/workflows/rnaseq/main.nf
@@ -381,7 +381,8 @@ workflow RNASEQ {
 
             // Name sort BAM before passing to Salmon
             SAMTOOLS_SORT (
-                BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME.out.bam
+                BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME.out.bam,
+                ch_fasta.map { [ [:], it ] }
             )
 
             // Only run prepare_for_rsem.py on paired-end BAM files