Merge branch 'main' into dev

CHANGELOG.md

@@ -3,6 +3,12 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [[1.1.3](https://github.com/sanger-tol/variantcalling/releases/tag/1.1.3)] - Shang Tang (patch 3) - [2024-05-24]
+
+### Enhancements & fixes
+
+- Fixed the bug in the filtering of multiple PacBio files
+
 ## [[1.1.2](https://github.com/sanger-tol/variantcalling/releases/tag/1.1.2)] - Shang Tang (patch 2) - [2024-03-14]
 
 ### Enhancements & fixes

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

nextflow.config

@@ -215,7 +215,7 @@ manifest {
     description     = """Variant calling pipeline for PacBio data using DeepVariant"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.10.1'
-    version = '1.1.2'
+    version = '1.1.3'
     doi             = 'https://doi.org/10.5281/zenodo.7890527'
 }
 

subworkflows/local/filter_pacbio.nf

@@ -61,9 +61,18 @@ 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() )