From 9db5259b8f92b98fea511fca168db7d232560d02 Mon Sep 17 00:00:00 2001 From: Guoying Qi Date: Fri, 24 May 2024 10:36:05 +0100 Subject: [PATCH 1/4] Fixed the bug in the filtering of multiple PacBio files --- CHANGELOG.md | 6 ++++++ modules/local/pacbio_filter.nf | 4 ++-- nextflow.config | 2 +- subworkflows/local/filter_pacbio.nf | 11 ++++++++++- 4 files changed, 19 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index d111be4..6e86a71 100644 --- a/CHANGELOG.md +++ b/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). +## [[1.2.2](https://github.com/sanger-tol/readmapping/releases/tag/1.1.3)] - Shang Tang (patch 2) - [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 diff --git a/modules/local/pacbio_filter.nf b/modules/local/pacbio_filter.nf index 18dd11c..8ff62e0 100644 --- 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/nextflow.config b/nextflow.config index ca837be..f67f186 100644 --- a/nextflow.config +++ b/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' } diff --git a/subworkflows/local/filter_pacbio.nf b/subworkflows/local/filter_pacbio.nf index 2e306bf..3f6916c 100644 --- a/subworkflows/local/filter_pacbio.nf +++ b/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() ) From cb1b188b8563fcb8bd5b12822578557e606a412c Mon Sep 17 00:00:00 2001 From: Matthieu Muffato Date: Fri, 24 May 2024 11:18:02 +0100 Subject: [PATCH 2/4] Typo --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 6e86a71..50c82f6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ 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). -## [[1.2.2](https://github.com/sanger-tol/readmapping/releases/tag/1.1.3)] - Shang Tang (patch 2) - [2024-05-24] +## [[1.1.3](https://github.com/sanger-tol/readmapping/releases/tag/1.1.3)] - Shang Tang (patch 2) - [2024-05-24] ### Enhancements & fixes From 1681ccee0fd8262c7a3ecf5026c16c260ae432e5 Mon Sep 17 00:00:00 2001 From: Matthieu Muffato Date: Fri, 24 May 2024 11:22:25 +0100 Subject: [PATCH 3/4] Typo --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 50c82f6..701d5fe 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ 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/readmapping/releases/tag/1.1.3)] - Shang Tang (patch 2) - [2024-05-24] +## [[1.1.3](https://github.com/sanger-tol/readmapping/releases/tag/1.1.3)] - Shang Tang (patch 3) - [2024-05-24] ### Enhancements & fixes From fba4492bd6da71e72684eff2da54c69c83122f52 Mon Sep 17 00:00:00 2001 From: Guoying Qi Date: Fri, 24 May 2024 11:26:01 +0100 Subject: [PATCH 4/4] typo again --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 701d5fe..c2764ae 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ 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/readmapping/releases/tag/1.1.3)] - Shang Tang (patch 3) - [2024-05-24] +## [[1.1.3](https://github.com/sanger-tol/variantcalling/releases/tag/1.1.3)] - Shang Tang (patch 3) - [2024-05-24] ### Enhancements & fixes