bugfix: pair each blocklist with its BAM file

sanger-tol · Feb 9, 2024 · fd4f989 · fd4f989
1 parent ccf3f63
commit fd4f989
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Showing 2 changed files with 12 additions and 3 deletions.
diff --git a/modules/local/pacbio_filter.nf b/modules/local/pacbio_filter.nf
@@ -11,8 +11,8 @@ process PACBIO_FILTER {
     tuple val(meta), path(txt)
 
     output:
-    path("*.blocklist"),  emit: list
-    path  "versions.yml", emit: versions
+    tuple val(meta), path("*.blocklist"), emit: list
+    path  "versions.yml"                , emit: versions
 
     when:
     task.ext.when == null || task.ext.when

diff --git a/subworkflows/local/filter_pacbio.nf b/subworkflows/local/filter_pacbio.nf
@@ -60,9 +60,18 @@ workflow FILTER_PACBIO {
     // Create filtered BAM file
     SAMTOOLS_CONVERT.out.bam
     | join ( SAMTOOLS_CONVERT.out.csi )
+    | join ( PACBIO_FILTER.out.list )
+    | set { ch_reads_and_list }
+
+    ch_reads_and_list
+    | map { meta, bam, csi, list -> [meta, bam, csi] }
     | set { ch_reads }
 
-    SAMTOOLS_FILTER ( ch_reads, [ [], [] ], PACBIO_FILTER.out.list )
+    ch_reads_and_list
+    | map { meta, bam, csi, list -> list }
+    | set { ch_lists }
+
+    SAMTOOLS_FILTER ( ch_reads, [ [], [] ], ch_lists )
     ch_versions = ch_versions.mix ( SAMTOOLS_FILTER.out.versions.first() )