From 950700bcdc0e9a2b6883d40d2c51c6fc435cd714 Mon Sep 17 00:00:00 2001 From: FriederikeHanssen Date: Mon, 28 Feb 2022 23:13:11 +0100 Subject: [PATCH] Update samtools version (#1361) * Update samtools version * update checksums --- modules/bwa/mem/main.nf | 6 +++--- modules/bwa/sampe/main.nf | 6 +++--- modules/bwa/samse/main.nf | 6 +++--- modules/bwamem2/mem/main.nf | 6 +++--- modules/custom/getchromsizes/main.nf | 6 +++--- modules/qualimap/bamqccram/main.nf | 6 +++--- tests/modules/bwa/sampe/test.yml | 2 +- tests/modules/bwa/samse/test.yml | 2 +- 8 files changed, 20 insertions(+), 20 deletions(-) diff --git a/modules/bwa/mem/main.nf b/modules/bwa/mem/main.nf index 9a91c77f..27ea6f42 100644 --- a/modules/bwa/mem/main.nf +++ b/modules/bwa/mem/main.nf @@ -2,10 +2,10 @@ process BWA_MEM { tag "$meta.id" label 'process_high' - conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.12" : null) + conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.15" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:66ed1b38d280722529bb8a0167b0cf02f8a0b488-0' : - 'quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:66ed1b38d280722529bb8a0167b0cf02f8a0b488-0' }" + 'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:c56a3aabc8d64e52d5b9da1e8ecec2031668596d-0' : + 'quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:c56a3aabc8d64e52d5b9da1e8ecec2031668596d-0' }" input: tuple val(meta), path(reads) diff --git a/modules/bwa/sampe/main.nf b/modules/bwa/sampe/main.nf index e781679e..73345d81 100644 --- a/modules/bwa/sampe/main.nf +++ b/modules/bwa/sampe/main.nf @@ -2,10 +2,10 @@ process BWA_SAMPE { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.12" : null) + conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.15" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:66ed1b38d280722529bb8a0167b0cf02f8a0b488-0' : - 'quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:66ed1b38d280722529bb8a0167b0cf02f8a0b488-0' }" + 'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:c56a3aabc8d64e52d5b9da1e8ecec2031668596d-0' : + 'quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:c56a3aabc8d64e52d5b9da1e8ecec2031668596d-0' }" input: tuple val(meta), path(reads), path(sai) diff --git a/modules/bwa/samse/main.nf b/modules/bwa/samse/main.nf index ac04c739..2c327d99 100644 --- a/modules/bwa/samse/main.nf +++ b/modules/bwa/samse/main.nf @@ -2,10 +2,10 @@ process BWA_SAMSE { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.12" : null) + conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.15" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:66ed1b38d280722529bb8a0167b0cf02f8a0b488-0' : - 'quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:66ed1b38d280722529bb8a0167b0cf02f8a0b488-0' }" + 'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:c56a3aabc8d64e52d5b9da1e8ecec2031668596d-0' : + 'quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:c56a3aabc8d64e52d5b9da1e8ecec2031668596d-0' }" input: tuple val(meta), path(reads), path(sai) diff --git a/modules/bwamem2/mem/main.nf b/modules/bwamem2/mem/main.nf index 56f595ec..21dfb1d6 100644 --- a/modules/bwamem2/mem/main.nf +++ b/modules/bwamem2/mem/main.nf @@ -2,10 +2,10 @@ process BWAMEM2_MEM { tag "$meta.id" label 'process_high' - conda (params.enable_conda ? "bioconda::bwa-mem2=2.2.1 bioconda::samtools=1.12" : null) + conda (params.enable_conda ? "bioconda::bwa-mem2=2.2.1 bioconda::samtools=1.15" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:cf603b12db30ec91daa04ba45a8ee0f35bbcd1e2-0' : - 'quay.io/biocontainers/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:cf603b12db30ec91daa04ba45a8ee0f35bbcd1e2-0' }" + 'https://depot.galaxyproject.org/singularity/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:8ee25ae85d7a2bacac3e3139db209aff3d605a18-0' : + 'quay.io/biocontainers/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:8ee25ae85d7a2bacac3e3139db209aff3d605a18-0' }" input: tuple val(meta), path(reads) diff --git a/modules/custom/getchromsizes/main.nf b/modules/custom/getchromsizes/main.nf index 39da7d34..bbcfa9be 100644 --- a/modules/custom/getchromsizes/main.nf +++ b/modules/custom/getchromsizes/main.nf @@ -2,10 +2,10 @@ process CUSTOM_GETCHROMSIZES { tag "$fasta" label 'process_low' - conda (params.enable_conda ? "bioconda::samtools=1.14" : null) + conda (params.enable_conda ? "bioconda::samtools=1.15" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' : - 'quay.io/biocontainers/samtools:1.14--hb421002_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' : + 'quay.io/biocontainers/samtools:1.15--h1170115_1' }" input: path fasta diff --git a/modules/qualimap/bamqccram/main.nf b/modules/qualimap/bamqccram/main.nf index b9a5538d..ab3fd51a 100644 --- a/modules/qualimap/bamqccram/main.nf +++ b/modules/qualimap/bamqccram/main.nf @@ -2,10 +2,10 @@ process QUALIMAP_BAMQCCRAM { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::qualimap=2.2.2d bioconda::samtools=1.12" : null) + conda (params.enable_conda ? "bioconda::qualimap=2.2.2d bioconda::samtools=1.15" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:4bf11d12f2c3eccf1eb585097c0b6fd31c18c418-0' : - 'quay.io/biocontainers/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:4bf11d12f2c3eccf1eb585097c0b6fd31c18c418-0' }" + 'https://depot.galaxyproject.org/singularity/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:9838874d42d4477d5042782ee019cec9854da7d5-0' : + 'quay.io/biocontainers/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:9838874d42d4477d5042782ee019cec9854da7d5-0' }" input: tuple val(meta), path(cram), path(crai) diff --git a/tests/modules/bwa/sampe/test.yml b/tests/modules/bwa/sampe/test.yml index fb6d7708..bf221ebc 100644 --- a/tests/modules/bwa/sampe/test.yml +++ b/tests/modules/bwa/sampe/test.yml @@ -5,4 +5,4 @@ - bwa/sampe files: - path: output/bwa/test.bam - md5sum: f6ad85d66d44c5d26e692109d2e34100 + md5sum: 01d1d71c88b6de07ed51d1d06e9e970b diff --git a/tests/modules/bwa/samse/test.yml b/tests/modules/bwa/samse/test.yml index 5a2fe1e3..c45f69dc 100644 --- a/tests/modules/bwa/samse/test.yml +++ b/tests/modules/bwa/samse/test.yml @@ -5,4 +5,4 @@ - bwa/samse files: - path: output/bwa/test.bam - md5sum: 27eb91146e45dee65664c18596be4262 + md5sum: ddfa4a8f6b65d44704a2d9528abc7e79