fixing se bam name sorting for genrich

samuelruizperez · Aug 15, 2023 · 238f781 · 238f781
1 parent 3932ea2
commit 238f781
Showing 1 changed file with 6 additions and 4 deletions.
diff --git a/subworkflows/local/bam_nofilter_bamtools.nf b/subworkflows/local/bam_nofilter_bamtools.nf
@@ -40,24 +40,26 @@ workflow BAM_NOFILTER_BAMTOOLS {
     ch_versions = ch_versions.mix(BAM_STATS_SAMTOOLS.out.versions.first())
 
     //
-    // Name sort PE BAM before filtering with pysam
+    // Name sort BAM
     //
     SAMTOOLS_SORT (
-        ch_bam_b.paired_end
+        ch_bam_b
     )
+    ch_bam_b_pe = SAMTOOLS_SORT.out.bam.paired_end
+    ch_bam_b_se = SAMTOOLS_SORT.out.bam.single_end
     ch_versions = ch_versions.mix(SAMTOOLS_SORT.out.versions.first())
 
     //
     // Sort, index PE BAM file and run samtools stats, flagstat and idxstats
     //
     BAM_SORT_STATS_SAMTOOLS (
-        SAMTOOLS_SORT.out.bam,
+        ch_bam_b_pe,
         ch_fasta
     )
     ch_versions = ch_versions.mix(BAM_SORT_STATS_SAMTOOLS.out.versions.first())
 
     emit:
-    name_bam = SAMTOOLS_SORT.out.bam.mix(ch_bam_b.single_end)                            // channel: [ val(meta), [ bam ] ]
+    name_bam = ch_bam_b_pe.mix(ch_bam_b_se.single_end)                                   // channel: [ val(meta), [ bam ] ]
     bam      = BAM_SORT_STATS_SAMTOOLS.out.bam.mix(ch_bam_b.single_end)                  // channel: [ val(meta), [ bam ] ]
     stats    = BAM_SORT_STATS_SAMTOOLS.out.stats.mix(BAM_STATS_SAMTOOLS.out.stats)       // channel: [ val(meta), [ stats ] ]
     flagstat = BAM_SORT_STATS_SAMTOOLS.out.flagstat.mix(BAM_STATS_SAMTOOLS.out.flagstat) // channel: [ val(meta), [ flagstat ] ]