From d6158726cac2b88007b3228d8e438d255db4220a Mon Sep 17 00:00:00 2001 From: Paolo Cozzi Date: Mon, 18 Dec 2023 17:29:01 +0100 Subject: [PATCH] :arrow_up: update freebayes module --- modules/cnr-ibba/freebayes/chunk/environment.yml | 2 +- modules/cnr-ibba/freebayes/chunk/main.nf | 4 ++-- modules/cnr-ibba/freebayes/multi/environment.yml | 2 +- modules/cnr-ibba/freebayes/multi/main.nf | 2 +- modules/cnr-ibba/freebayes/single/environment.yml | 2 +- modules/cnr-ibba/freebayes/single/main.nf | 4 ++-- modules/cnr-ibba/freebayes/splitbam/environment.yml | 2 +- modules/cnr-ibba/freebayes/splitbam/main.nf | 4 ++-- tests/modules/cnr-ibba/freebayes/chunk/test.yml | 4 ++-- 9 files changed, 13 insertions(+), 13 deletions(-) diff --git a/modules/cnr-ibba/freebayes/chunk/environment.yml b/modules/cnr-ibba/freebayes/chunk/environment.yml index f583435..64411d9 100644 --- a/modules/cnr-ibba/freebayes/chunk/environment.yml +++ b/modules/cnr-ibba/freebayes/chunk/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::freebayes=1.3.6 + - bioconda::freebayes=1.3.7 diff --git a/modules/cnr-ibba/freebayes/chunk/main.nf b/modules/cnr-ibba/freebayes/chunk/main.nf index f6aafff..83389bb 100644 --- a/modules/cnr-ibba/freebayes/chunk/main.nf +++ b/modules/cnr-ibba/freebayes/chunk/main.nf @@ -6,8 +6,8 @@ process FREEBAYES_CHUNK { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/freebayes:1.3.6--hb089aa1_0': - 'biocontainers/freebayes:1.3.6--hb089aa1_0' }" + 'https://depot.galaxyproject.org/singularity/freebayes:1.3.7--h1870644_0': + 'biocontainers/freebayes:1.3.7--h1870644_0' }" input: tuple val(meta), val(region) diff --git a/modules/cnr-ibba/freebayes/multi/environment.yml b/modules/cnr-ibba/freebayes/multi/environment.yml index bb8e562..c06d21e 100644 --- a/modules/cnr-ibba/freebayes/multi/environment.yml +++ b/modules/cnr-ibba/freebayes/multi/environment.yml @@ -4,6 +4,6 @@ channels: - bioconda - defaults dependencies: - - bioconda::freebayes=1.3.6 + - bioconda::freebayes=1.3.7 - main::numpy - main::scipy diff --git a/modules/cnr-ibba/freebayes/multi/main.nf b/modules/cnr-ibba/freebayes/multi/main.nf index 114bebf..9dc8017 100644 --- a/modules/cnr-ibba/freebayes/multi/main.nf +++ b/modules/cnr-ibba/freebayes/multi/main.nf @@ -4,7 +4,7 @@ process FREEBAYES_MULTI { label 'process_high' conda "${moduleDir}/environment.yml" - container "docker.io/bunop/freebayes:v0.1" + container "docker.io/bunop/freebayes:v0.2" input: tuple val(meta), path(bam) diff --git a/modules/cnr-ibba/freebayes/single/environment.yml b/modules/cnr-ibba/freebayes/single/environment.yml index 4c99799..925db34 100644 --- a/modules/cnr-ibba/freebayes/single/environment.yml +++ b/modules/cnr-ibba/freebayes/single/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::freebayes=1.3.6 + - bioconda::freebayes=1.3.7 diff --git a/modules/cnr-ibba/freebayes/single/main.nf b/modules/cnr-ibba/freebayes/single/main.nf index e1ea7c1..63f8507 100644 --- a/modules/cnr-ibba/freebayes/single/main.nf +++ b/modules/cnr-ibba/freebayes/single/main.nf @@ -5,8 +5,8 @@ process FREEBAYES_SINGLE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/freebayes:1.3.6--hb089aa1_0': - 'biocontainers/freebayes:1.3.6--hb089aa1_0' }" + 'https://depot.galaxyproject.org/singularity/freebayes:1.3.7--h1870644_0': + 'biocontainers/freebayes:1.3.7--h1870644_0' }" input: tuple val(meta), path(bam), path(bai) diff --git a/modules/cnr-ibba/freebayes/splitbam/environment.yml b/modules/cnr-ibba/freebayes/splitbam/environment.yml index b2ff92c..97bbf0b 100644 --- a/modules/cnr-ibba/freebayes/splitbam/environment.yml +++ b/modules/cnr-ibba/freebayes/splitbam/environment.yml @@ -4,6 +4,6 @@ channels: - bioconda - defaults dependencies: - - bioconda::freebayes=1.3.6 + - bioconda::freebayes=1.3.7 - main::numpy - main::scipy diff --git a/modules/cnr-ibba/freebayes/splitbam/main.nf b/modules/cnr-ibba/freebayes/splitbam/main.nf index 5903444..2ba3a94 100644 --- a/modules/cnr-ibba/freebayes/splitbam/main.nf +++ b/modules/cnr-ibba/freebayes/splitbam/main.nf @@ -4,7 +4,7 @@ process FREEBAYES_SPLITBAM { label 'process_single' conda "${moduleDir}/environment.yml" - container "docker.io/bunop/freebayes:v0.1" + container "docker.io/bunop/freebayes:v0.2" input: tuple val(meta), path(bam) @@ -25,7 +25,7 @@ process FREEBAYES_SPLITBAM { def prefix = task.ext.prefix ?: "${meta.id}" """ - ls $bam | xargs -n1 > ${prefix}.list.txt + ls $bam | sort | xargs -n1 > ${prefix}.list.txt split_ref_by_bai_datasize.py \\ --bam-list ${prefix}.list.txt \\ diff --git a/tests/modules/cnr-ibba/freebayes/chunk/test.yml b/tests/modules/cnr-ibba/freebayes/chunk/test.yml index 3f6d637..26c7854 100644 --- a/tests/modules/cnr-ibba/freebayes/chunk/test.yml +++ b/tests/modules/cnr-ibba/freebayes/chunk/test.yml @@ -9,6 +9,6 @@ - path: output/freebayes/all.fb.regions.txt md5sum: e4cd6cbdb91d5205fcefcc7bc068d3e5 - path: output/freebayes/chr22:0-40001.vcf.gz - md5sum: fba544980eebf86c66460c40f48d7809 + md5sum: 709872fc2910431b1e8b7074bfe38c67 - path: output/freebayes/chr22:0-40001.vcf.gz.tbi - md5sum: 83b1d5e5b36d61529d9d2d69cd4babc5 + md5sum: 4cb176febbc8c26d717a6c6e67b9c905