From d853d050c8f957dedc7644792c69b5b0a4db49a7 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Thu, 27 Feb 2025 09:49:24 +0000 Subject: [PATCH 1/6] BBMAP updates --- modules/nf-core/bbmap/align/environment.yml | 6 +++--- modules/nf-core/bbmap/align/main.nf | 4 ++-- modules/nf-core/bbmap/bbduk/environment.yml | 2 +- modules/nf-core/bbmap/bbduk/main.nf | 4 ++-- modules/nf-core/bbmap/bbmerge/environment.yml | 2 +- modules/nf-core/bbmap/bbmerge/main.nf | 4 ++-- modules/nf-core/bbmap/bbnorm/environment.yml | 4 ++-- modules/nf-core/bbmap/bbnorm/main.nf | 5 ++--- modules/nf-core/bbmap/bbsplit/environment.yml | 2 +- modules/nf-core/bbmap/bbsplit/main.nf | 4 ++-- modules/nf-core/bbmap/clumpify/environment.yml | 2 +- modules/nf-core/bbmap/clumpify/main.nf | 4 ++-- modules/nf-core/bbmap/filterbyname/environment.yml | 2 +- modules/nf-core/bbmap/filterbyname/main.nf | 4 ++-- modules/nf-core/bbmap/index/environment.yml | 2 +- modules/nf-core/bbmap/index/main.nf | 4 ++-- modules/nf-core/bbmap/pileup/environment.yml | 6 +++--- modules/nf-core/bbmap/pileup/main.nf | 4 ++-- modules/nf-core/bbmap/repair/environment.yml | 2 +- modules/nf-core/bbmap/repair/main.nf | 4 ++-- modules/nf-core/bbmap/sendsketch/environment.yml | 2 +- modules/nf-core/bbmap/sendsketch/main.nf | 4 ++-- 22 files changed, 38 insertions(+), 39 deletions(-) diff --git a/modules/nf-core/bbmap/align/environment.yml b/modules/nf-core/bbmap/align/environment.yml index 977fb4ba4a4..3a85a9f417c 100644 --- a/modules/nf-core/bbmap/align/environment.yml +++ b/modules/nf-core/bbmap/align/environment.yml @@ -4,6 +4,6 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::bbmap=39.01 - - bioconda::samtools=1.16.1 - - pigz=2.6 + - bioconda::bbmap=39.17 + - bioconda::samtools=1.21 + - pigz=2.8 diff --git a/modules/nf-core/bbmap/align/main.nf b/modules/nf-core/bbmap/align/main.nf index c4e7acf7bde..2191d307325 100644 --- a/modules/nf-core/bbmap/align/main.nf +++ b/modules/nf-core/bbmap/align/main.nf @@ -4,8 +4,8 @@ process BBMAP_ALIGN { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:e8a286b2e789c091bac0a57302cdc78aa0112353-0' : - 'biocontainers/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:e8a286b2e789c091bac0a57302cdc78aa0112353-0' }" + 'oras://community.wave.seqera.io/library/bbmap_samtools_pigz:2a066f0214cc5eb0' : + 'community.wave.seqera.io/library/bbmap_samtools_pigz:79703e935236b43b' }" input: tuple val(meta), path(fastq) diff --git a/modules/nf-core/bbmap/bbduk/environment.yml b/modules/nf-core/bbmap/bbduk/environment.yml index f76f417a31b..fcb70a806cb 100644 --- a/modules/nf-core/bbmap/bbduk/environment.yml +++ b/modules/nf-core/bbmap/bbduk/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::bbmap=39.10 + - bioconda::bbmap=39.17 diff --git a/modules/nf-core/bbmap/bbduk/main.nf b/modules/nf-core/bbmap/bbduk/main.nf index 00bbdedad0e..21e6d769990 100644 --- a/modules/nf-core/bbmap/bbduk/main.nf +++ b/modules/nf-core/bbmap/bbduk/main.nf @@ -4,8 +4,8 @@ process BBMAP_BBDUK { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bbmap:39.10--h92535d8_0': - 'biocontainers/bbmap:39.10--h92535d8_0' }" + 'https://depot.galaxyproject.org/singularity/bbmap:39.17-h44cf5ac_0': + 'biocontainers/bbmap:39.17-h44cf5ac_0' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bbmap/bbmerge/environment.yml b/modules/nf-core/bbmap/bbmerge/environment.yml index f76f417a31b..fcb70a806cb 100644 --- a/modules/nf-core/bbmap/bbmerge/environment.yml +++ b/modules/nf-core/bbmap/bbmerge/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::bbmap=39.10 + - bioconda::bbmap=39.17 diff --git a/modules/nf-core/bbmap/bbmerge/main.nf b/modules/nf-core/bbmap/bbmerge/main.nf index 12cdd456805..06e619ce1f0 100644 --- a/modules/nf-core/bbmap/bbmerge/main.nf +++ b/modules/nf-core/bbmap/bbmerge/main.nf @@ -3,8 +3,8 @@ process BBMAP_BBMERGE { label 'process_single' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bbmap:39.10--h92535d8_0': - 'biocontainers/bbmap:39.10--h92535d8_0' }" + 'https://depot.galaxyproject.org/singularity/bbmap:39.17-h44cf5ac_0': + 'biocontainers/bbmap:39.17-h44cf5ac_0' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bbmap/bbnorm/environment.yml b/modules/nf-core/bbmap/bbnorm/environment.yml index 5dfe793f98e..3f77ff21af7 100644 --- a/modules/nf-core/bbmap/bbnorm/environment.yml +++ b/modules/nf-core/bbmap/bbnorm/environment.yml @@ -4,5 +4,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::bbmap=39.01 - - pigz=2.6 + - bioconda::bbmap=39.17 + - pigz=2.8 diff --git a/modules/nf-core/bbmap/bbnorm/main.nf b/modules/nf-core/bbmap/bbnorm/main.nf index 1cac93de0b7..d56e5c46168 100644 --- a/modules/nf-core/bbmap/bbnorm/main.nf +++ b/modules/nf-core/bbmap/bbnorm/main.nf @@ -4,9 +4,8 @@ process BBMAP_BBNORM { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:e8a286b2e789c091bac0a57302cdc78aa0112353-0': - 'biocontainers/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:e8a286b2e789c091bac0a57302cdc78aa0112353-0' }" - + 'oras://community.wave.seqera.io/library/bbmap_samtools_pigz:2a066f0214cc5eb0' : + 'community.wave.seqera.io/library/bbmap_samtools_pigz:79703e935236b43b' }" input: tuple val(meta), path(fastq) diff --git a/modules/nf-core/bbmap/bbsplit/environment.yml b/modules/nf-core/bbmap/bbsplit/environment.yml index f76f417a31b..fcb70a806cb 100644 --- a/modules/nf-core/bbmap/bbsplit/environment.yml +++ b/modules/nf-core/bbmap/bbsplit/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::bbmap=39.10 + - bioconda::bbmap=39.17 diff --git a/modules/nf-core/bbmap/bbsplit/main.nf b/modules/nf-core/bbmap/bbsplit/main.nf index 9eb53208c4d..5e09d4af9fd 100644 --- a/modules/nf-core/bbmap/bbsplit/main.nf +++ b/modules/nf-core/bbmap/bbsplit/main.nf @@ -5,8 +5,8 @@ process BBMAP_BBSPLIT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bbmap:39.10--h92535d8_0': - 'biocontainers/bbmap:39.10--h92535d8_0' }" + 'https://depot.galaxyproject.org/singularity/bbmap:39.17-h44cf5ac_0': + 'biocontainers/bbmap:39.17-h44cf5ac_0' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bbmap/clumpify/environment.yml b/modules/nf-core/bbmap/clumpify/environment.yml index f76f417a31b..fcb70a806cb 100644 --- a/modules/nf-core/bbmap/clumpify/environment.yml +++ b/modules/nf-core/bbmap/clumpify/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::bbmap=39.10 + - bioconda::bbmap=39.17 diff --git a/modules/nf-core/bbmap/clumpify/main.nf b/modules/nf-core/bbmap/clumpify/main.nf index fc6a85ad635..e4fefa1e12c 100644 --- a/modules/nf-core/bbmap/clumpify/main.nf +++ b/modules/nf-core/bbmap/clumpify/main.nf @@ -5,8 +5,8 @@ process BBMAP_CLUMPIFY { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bbmap:39.10--h92535d8_0': - 'biocontainers/bbmap:39.10--h92535d8_0' }" + 'https://depot.galaxyproject.org/singularity/bbmap:39.17-h44cf5ac_0': + 'biocontainers/bbmap:39.17-h44cf5ac_0' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bbmap/filterbyname/environment.yml b/modules/nf-core/bbmap/filterbyname/environment.yml index f76f417a31b..fcb70a806cb 100644 --- a/modules/nf-core/bbmap/filterbyname/environment.yml +++ b/modules/nf-core/bbmap/filterbyname/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::bbmap=39.10 + - bioconda::bbmap=39.17 diff --git a/modules/nf-core/bbmap/filterbyname/main.nf b/modules/nf-core/bbmap/filterbyname/main.nf index 4c6af276ceb..c4c85270e05 100644 --- a/modules/nf-core/bbmap/filterbyname/main.nf +++ b/modules/nf-core/bbmap/filterbyname/main.nf @@ -4,8 +4,8 @@ process BBMAP_FILTERBYNAME { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bbmap:39.10--h92535d8_0': - 'biocontainers/bbmap:39.10--h92535d8_0' }" + 'https://depot.galaxyproject.org/singularity/bbmap:39.17-h44cf5ac_0': + 'biocontainers/bbmap:39.17-h44cf5ac_0' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bbmap/index/environment.yml b/modules/nf-core/bbmap/index/environment.yml index f76f417a31b..fcb70a806cb 100644 --- a/modules/nf-core/bbmap/index/environment.yml +++ b/modules/nf-core/bbmap/index/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::bbmap=39.10 + - bioconda::bbmap=39.17 diff --git a/modules/nf-core/bbmap/index/main.nf b/modules/nf-core/bbmap/index/main.nf index e7b3eb113e5..c15654ddb42 100644 --- a/modules/nf-core/bbmap/index/main.nf +++ b/modules/nf-core/bbmap/index/main.nf @@ -4,8 +4,8 @@ process BBMAP_INDEX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bbmap:39.10--h92535d8_0': - 'biocontainers/bbmap:39.10--h92535d8_0' }" + 'https://depot.galaxyproject.org/singularity/bbmap:39.17-h44cf5ac_0': + 'biocontainers/bbmap:39.17-h44cf5ac_0' }" input: path fasta diff --git a/modules/nf-core/bbmap/pileup/environment.yml b/modules/nf-core/bbmap/pileup/environment.yml index 977fb4ba4a4..3a85a9f417c 100644 --- a/modules/nf-core/bbmap/pileup/environment.yml +++ b/modules/nf-core/bbmap/pileup/environment.yml @@ -4,6 +4,6 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::bbmap=39.01 - - bioconda::samtools=1.16.1 - - pigz=2.6 + - bioconda::bbmap=39.17 + - bioconda::samtools=1.21 + - pigz=2.8 diff --git a/modules/nf-core/bbmap/pileup/main.nf b/modules/nf-core/bbmap/pileup/main.nf index 6f3b1aa7a60..f498805dc1b 100644 --- a/modules/nf-core/bbmap/pileup/main.nf +++ b/modules/nf-core/bbmap/pileup/main.nf @@ -4,8 +4,8 @@ process BBMAP_PILEUP { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:e8a286b2e789c091bac0a57302cdc78aa0112353-0' : - 'biocontainers/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:e8a286b2e789c091bac0a57302cdc78aa0112353-0' }" + 'oras://community.wave.seqera.io/library/bbmap_samtools_pigz:2a066f0214cc5eb0' : + 'community.wave.seqera.io/library/bbmap_samtools_pigz:79703e935236b43b' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/bbmap/repair/environment.yml b/modules/nf-core/bbmap/repair/environment.yml index b609e090138..fcb70a806cb 100644 --- a/modules/nf-core/bbmap/repair/environment.yml +++ b/modules/nf-core/bbmap/repair/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::bbmap=39.13 + - bioconda::bbmap=39.17 diff --git a/modules/nf-core/bbmap/repair/main.nf b/modules/nf-core/bbmap/repair/main.nf index ec868fa7270..38080c04cce 100644 --- a/modules/nf-core/bbmap/repair/main.nf +++ b/modules/nf-core/bbmap/repair/main.nf @@ -3,8 +3,8 @@ process BBMAP_REPAIR { label 'process_single' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bbmap:39.13--he5f24ec_1': - 'biocontainers/bbmap:39.13--he5f24ec_1' }" + 'https://depot.galaxyproject.org/singularity/bbmap:39.17-h44cf5ac_0': + 'biocontainers/bbmap:39.17-h44cf5ac_0' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bbmap/sendsketch/environment.yml b/modules/nf-core/bbmap/sendsketch/environment.yml index f76f417a31b..fcb70a806cb 100644 --- a/modules/nf-core/bbmap/sendsketch/environment.yml +++ b/modules/nf-core/bbmap/sendsketch/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::bbmap=39.10 + - bioconda::bbmap=39.17 diff --git a/modules/nf-core/bbmap/sendsketch/main.nf b/modules/nf-core/bbmap/sendsketch/main.nf index 5b3a2668a72..e10b0b7614c 100644 --- a/modules/nf-core/bbmap/sendsketch/main.nf +++ b/modules/nf-core/bbmap/sendsketch/main.nf @@ -4,8 +4,8 @@ process BBMAP_SENDSKETCH { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bbmap:39.10--h92535d8_0': - 'biocontainers/bbmap:39.10--h92535d8_0' }" + 'https://depot.galaxyproject.org/singularity/bbmap:39.17-h44cf5ac_0': + 'biocontainers/bbmap:39.17-h44cf5ac_0' }" input: tuple val(meta), path(file) From 2503b93a8d96d5cce7da6c61e4e4e50d02ecce5d Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Thu, 27 Feb 2025 09:57:58 +0000 Subject: [PATCH 2/6] Make the container urls correct --- modules/nf-core/bbmap/bbduk/main.nf | 4 ++-- modules/nf-core/bbmap/bbmerge/main.nf | 4 ++-- modules/nf-core/bbmap/bbsplit/main.nf | 4 ++-- modules/nf-core/bbmap/clumpify/main.nf | 4 ++-- modules/nf-core/bbmap/filterbyname/main.nf | 4 ++-- modules/nf-core/bbmap/index/main.nf | 4 ++-- modules/nf-core/bbmap/repair/main.nf | 4 ++-- modules/nf-core/bbmap/sendsketch/main.nf | 4 ++-- 8 files changed, 16 insertions(+), 16 deletions(-) diff --git a/modules/nf-core/bbmap/bbduk/main.nf b/modules/nf-core/bbmap/bbduk/main.nf index 21e6d769990..58a598bb1f5 100644 --- a/modules/nf-core/bbmap/bbduk/main.nf +++ b/modules/nf-core/bbmap/bbduk/main.nf @@ -4,8 +4,8 @@ process BBMAP_BBDUK { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bbmap:39.17-h44cf5ac_0': - 'biocontainers/bbmap:39.17-h44cf5ac_0' }" + 'https://depot.galaxyproject.org/singularity/bbmap:39.17--h44cf5ac_0': + 'biocontainers/bbmap:39.17--he5f24ec_0' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bbmap/bbmerge/main.nf b/modules/nf-core/bbmap/bbmerge/main.nf index 06e619ce1f0..52374b62e4c 100644 --- a/modules/nf-core/bbmap/bbmerge/main.nf +++ b/modules/nf-core/bbmap/bbmerge/main.nf @@ -3,8 +3,8 @@ process BBMAP_BBMERGE { label 'process_single' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bbmap:39.17-h44cf5ac_0': - 'biocontainers/bbmap:39.17-h44cf5ac_0' }" + 'https://depot.galaxyproject.org/singularity/bbmap:39.17--h44cf5ac_0': + 'biocontainers/bbmap:39.17--he5f24ec_0' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bbmap/bbsplit/main.nf b/modules/nf-core/bbmap/bbsplit/main.nf index 5e09d4af9fd..9e85cd78710 100644 --- a/modules/nf-core/bbmap/bbsplit/main.nf +++ b/modules/nf-core/bbmap/bbsplit/main.nf @@ -5,8 +5,8 @@ process BBMAP_BBSPLIT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bbmap:39.17-h44cf5ac_0': - 'biocontainers/bbmap:39.17-h44cf5ac_0' }" + 'https://depot.galaxyproject.org/singularity/bbmap:39.17--h44cf5ac_0': + 'biocontainers/bbmap:39.17--he5f24ec_0' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bbmap/clumpify/main.nf b/modules/nf-core/bbmap/clumpify/main.nf index e4fefa1e12c..59df170e255 100644 --- a/modules/nf-core/bbmap/clumpify/main.nf +++ b/modules/nf-core/bbmap/clumpify/main.nf @@ -5,8 +5,8 @@ process BBMAP_CLUMPIFY { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bbmap:39.17-h44cf5ac_0': - 'biocontainers/bbmap:39.17-h44cf5ac_0' }" + 'https://depot.galaxyproject.org/singularity/bbmap:39.17--h44cf5ac_0': + 'biocontainers/bbmap:39.17--he5f24ec_0' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bbmap/filterbyname/main.nf b/modules/nf-core/bbmap/filterbyname/main.nf index c4c85270e05..8612ff3f85d 100644 --- a/modules/nf-core/bbmap/filterbyname/main.nf +++ b/modules/nf-core/bbmap/filterbyname/main.nf @@ -4,8 +4,8 @@ process BBMAP_FILTERBYNAME { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bbmap:39.17-h44cf5ac_0': - 'biocontainers/bbmap:39.17-h44cf5ac_0' }" + 'https://depot.galaxyproject.org/singularity/bbmap:39.17--h44cf5ac_0': + 'biocontainers/bbmap:39.17--he5f24ec_0' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bbmap/index/main.nf b/modules/nf-core/bbmap/index/main.nf index c15654ddb42..7ab3a412c3a 100644 --- a/modules/nf-core/bbmap/index/main.nf +++ b/modules/nf-core/bbmap/index/main.nf @@ -4,8 +4,8 @@ process BBMAP_INDEX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bbmap:39.17-h44cf5ac_0': - 'biocontainers/bbmap:39.17-h44cf5ac_0' }" + 'https://depot.galaxyproject.org/singularity/bbmap:39.17--h44cf5ac_0': + 'biocontainers/bbmap:39.17--he5f24ec_0' }" input: path fasta diff --git a/modules/nf-core/bbmap/repair/main.nf b/modules/nf-core/bbmap/repair/main.nf index 38080c04cce..41845d85690 100644 --- a/modules/nf-core/bbmap/repair/main.nf +++ b/modules/nf-core/bbmap/repair/main.nf @@ -3,8 +3,8 @@ process BBMAP_REPAIR { label 'process_single' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bbmap:39.17-h44cf5ac_0': - 'biocontainers/bbmap:39.17-h44cf5ac_0' }" + 'https://depot.galaxyproject.org/singularity/bbmap:39.17--h44cf5ac_0': + 'biocontainers/bbmap:39.17--he5f24ec_0' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bbmap/sendsketch/main.nf b/modules/nf-core/bbmap/sendsketch/main.nf index e10b0b7614c..27664545054 100644 --- a/modules/nf-core/bbmap/sendsketch/main.nf +++ b/modules/nf-core/bbmap/sendsketch/main.nf @@ -4,8 +4,8 @@ process BBMAP_SENDSKETCH { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bbmap:39.17-h44cf5ac_0': - 'biocontainers/bbmap:39.17-h44cf5ac_0' }" + 'https://depot.galaxyproject.org/singularity/bbmap:39.17--h44cf5ac_0': + 'biocontainers/bbmap:39.17--he5f24ec_0' }" input: tuple val(meta), path(file) From 9345e6f890e20efeb47ce901c2d93b367caa3213 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Thu, 27 Feb 2025 10:07:15 +0000 Subject: [PATCH 3/6] Four tests more --- .../bbmap/align/tests/main.nf.test.snap | 12 ++++++------ .../bbmap/bbduk/tests/main.nf.test.snap | 18 +++++++++--------- .../bbmap/bbmerge/tests/main.nf.test.snap | 14 +++++++------- .../bbmap/bbnorm/tests/main.nf.test.snap | 12 ++++++------ 4 files changed, 28 insertions(+), 28 deletions(-) diff --git a/modules/nf-core/bbmap/align/tests/main.nf.test.snap b/modules/nf-core/bbmap/align/tests/main.nf.test.snap index 2423ad444e3..9580cbc484d 100644 --- a/modules/nf-core/bbmap/align/tests/main.nf.test.snap +++ b/modules/nf-core/bbmap/align/tests/main.nf.test.snap @@ -6,7 +6,7 @@ "c17efa4ccc4e9018090792c71af92660" ], [ - "versions.yml:md5,7c9a1c72ae9ea9c54b7518e96f8f89bb" + "versions.yml:md5,87adfd2a4838916a43a45f15b30df5e7" ] ], "meta": { @@ -22,7 +22,7 @@ "88d78879c34214288644aec7ec3cb270" ], [ - "versions.yml:md5,7c9a1c72ae9ea9c54b7518e96f8f89bb" + "versions.yml:md5,87adfd2a4838916a43a45f15b30df5e7" ] ], "meta": { @@ -38,7 +38,7 @@ "88d78879c34214288644aec7ec3cb270" ], [ - "versions.yml:md5,7c9a1c72ae9ea9c54b7518e96f8f89bb" + "versions.yml:md5,87adfd2a4838916a43a45f15b30df5e7" ] ], "meta": { @@ -54,7 +54,7 @@ "88d78879c34214288644aec7ec3cb270" ], [ - "versions.yml:md5,7c9a1c72ae9ea9c54b7518e96f8f89bb" + "versions.yml:md5,87adfd2a4838916a43a45f15b30df5e7" ] ], "meta": { @@ -70,7 +70,7 @@ "d41d8cd98f00b204e9800998ecf8427e" ], [ - "versions.yml:md5,7c9a1c72ae9ea9c54b7518e96f8f89bb" + "versions.yml:md5,87adfd2a4838916a43a45f15b30df5e7" ] ], "meta": { @@ -79,4 +79,4 @@ }, "timestamp": "2025-01-08T21:06:47.377762689" } -} \ No newline at end of file +} diff --git a/modules/nf-core/bbmap/bbduk/tests/main.nf.test.snap b/modules/nf-core/bbmap/bbduk/tests/main.nf.test.snap index 258593ee872..a610ffa3701 100644 --- a/modules/nf-core/bbmap/bbduk/tests/main.nf.test.snap +++ b/modules/nf-core/bbmap/bbduk/tests/main.nf.test.snap @@ -14,7 +14,7 @@ ] ], [ - "versions.yml:md5,6d196411d38a3c3011a38e1a87c9203c" + "versions.yml:md5,9be1a40778615e00c3d8c615ced9f78e" ] ], "meta": { @@ -26,7 +26,7 @@ "sarscov2 - single end w/ contams [fastq,fasta] - fastq": { "content": [ [ - "versions.yml:md5,6d196411d38a3c3011a38e1a87c9203c" + "versions.yml:md5,9be1a40778615e00c3d8c615ced9f78e" ] ], "meta": { @@ -38,7 +38,7 @@ "sarscov2 - paired end w/ contams [fastq,fasta] - fastq": { "content": [ [ - "versions.yml:md5,6d196411d38a3c3011a38e1a87c9203c" + "versions.yml:md5,9be1a40778615e00c3d8c615ced9f78e" ] ], "meta": { @@ -72,7 +72,7 @@ ] ], "2": [ - "versions.yml:md5,6d196411d38a3c3011a38e1a87c9203c" + "versions.yml:md5,9be1a40778615e00c3d8c615ced9f78e" ], "log": [ [ @@ -96,7 +96,7 @@ ] ], "versions": [ - "versions.yml:md5,6d196411d38a3c3011a38e1a87c9203c" + "versions.yml:md5,9be1a40778615e00c3d8c615ced9f78e" ] } ], @@ -128,7 +128,7 @@ ] ], "2": [ - "versions.yml:md5,6d196411d38a3c3011a38e1a87c9203c" + "versions.yml:md5,9be1a40778615e00c3d8c615ced9f78e" ], "log": [ [ @@ -149,7 +149,7 @@ ] ], "versions": [ - "versions.yml:md5,6d196411d38a3c3011a38e1a87c9203c" + "versions.yml:md5,9be1a40778615e00c3d8c615ced9f78e" ] } ], @@ -171,7 +171,7 @@ ] ], [ - "versions.yml:md5,6d196411d38a3c3011a38e1a87c9203c" + "versions.yml:md5,9be1a40778615e00c3d8c615ced9f78e" ] ], "meta": { @@ -180,4 +180,4 @@ }, "timestamp": "2024-10-19T15:58:00.420305019" } -} \ No newline at end of file +} diff --git a/modules/nf-core/bbmap/bbmerge/tests/main.nf.test.snap b/modules/nf-core/bbmap/bbmerge/tests/main.nf.test.snap index d1b87f25824..3ae12f13996 100644 --- a/modules/nf-core/bbmap/bbmerge/tests/main.nf.test.snap +++ b/modules/nf-core/bbmap/bbmerge/tests/main.nf.test.snap @@ -2,7 +2,7 @@ "sarscov2_illumina_paired - fastq_gz": { "content": [ [ - "versions.yml:md5,d1f2c86a17024502b3f189ffc0f9dca2" + "versions.yml:md5,028b993458a013e6c60a5bba4a0a3be5" ] ], "meta": { @@ -42,7 +42,7 @@ ] ], "3": [ - "versions.yml:md5,d1f2c86a17024502b3f189ffc0f9dca2" + "versions.yml:md5,028b993458a013e6c60a5bba4a0a3be5" ], "4": [ "test.bbmerge.log:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -78,7 +78,7 @@ ] ], "versions": [ - "versions.yml:md5,d1f2c86a17024502b3f189ffc0f9dca2" + "versions.yml:md5,028b993458a013e6c60a5bba4a0a3be5" ] } ], @@ -91,7 +91,7 @@ "sarscov2_illumina_interleaved - fastq_gz": { "content": [ [ - "versions.yml:md5,d1f2c86a17024502b3f189ffc0f9dca2" + "versions.yml:md5,028b993458a013e6c60a5bba4a0a3be5" ] ], "meta": { @@ -134,7 +134,7 @@ ] ], "3": [ - "versions.yml:md5,d1f2c86a17024502b3f189ffc0f9dca2" + "versions.yml:md5,028b993458a013e6c60a5bba4a0a3be5" ], "4": [ "test.bbmerge.log:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -173,7 +173,7 @@ ] ], "versions": [ - "versions.yml:md5,d1f2c86a17024502b3f189ffc0f9dca2" + "versions.yml:md5,028b993458a013e6c60a5bba4a0a3be5" ] } ], @@ -183,4 +183,4 @@ }, "timestamp": "2024-10-19T16:01:24.272511838" } -} \ No newline at end of file +} diff --git a/modules/nf-core/bbmap/bbnorm/tests/main.nf.test.snap b/modules/nf-core/bbmap/bbnorm/tests/main.nf.test.snap index 1d7b2438abd..f124e7fc51c 100644 --- a/modules/nf-core/bbmap/bbnorm/tests/main.nf.test.snap +++ b/modules/nf-core/bbmap/bbnorm/tests/main.nf.test.snap @@ -10,7 +10,7 @@ ], "test.bbnorm.log", [ - "versions.yml:md5,90b331a3702d052d61e0a14189e3fc01" + "versions.yml:md5,1aee8175e324cb47f12450f2fae2b7c2" ] ], "meta": { @@ -30,7 +30,7 @@ ], "test.bbnorm.log", [ - "versions.yml:md5,90b331a3702d052d61e0a14189e3fc01" + "versions.yml:md5,1aee8175e324cb47f12450f2fae2b7c2" ] ], "meta": { @@ -53,7 +53,7 @@ ], "test.bbnorm.log", [ - "versions.yml:md5,90b331a3702d052d61e0a14189e3fc01" + "versions.yml:md5,1aee8175e324cb47f12450f2fae2b7c2" ] ], "meta": { @@ -65,11 +65,11 @@ "test-bbmap-bbnorm-se": { "content": [ [ - + ], "test.bbnorm.log", [ - "versions.yml:md5,90b331a3702d052d61e0a14189e3fc01" + "versions.yml:md5,1aee8175e324cb47f12450f2fae2b7c2" ] ], "meta": { @@ -78,4 +78,4 @@ }, "timestamp": "2024-08-26T14:59:16.676091" } -} \ No newline at end of file +} From d82815342c3a116f2124d9c034577b831aba7a2b Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Thu, 27 Feb 2025 10:19:55 +0000 Subject: [PATCH 4/6] Some more snapshots updated --- .../bbmap/bbsplit/tests/main.nf.test.snap | 38 +++++++++---------- .../bbmap/clumpify/tests/main.nf.test.snap | 6 +-- .../filterbyname/tests/main.nf.test.snap | 20 +++++----- 3 files changed, 32 insertions(+), 32 deletions(-) diff --git a/modules/nf-core/bbmap/bbsplit/tests/main.nf.test.snap b/modules/nf-core/bbmap/bbsplit/tests/main.nf.test.snap index 6bdc3c0d1e9..4df7b69b7a9 100644 --- a/modules/nf-core/bbmap/bbsplit/tests/main.nf.test.snap +++ b/modules/nf-core/bbmap/bbsplit/tests/main.nf.test.snap @@ -9,7 +9,7 @@ "namelist.txt:md5,45e7a4cdc7a11a39ada56844ca3a1e30" ], [ - "versions.yml:md5,97dfea8bc38fdb0ec800ee936e0c6e27" + "versions.yml:md5,0eaa29e412ac44532bebff0f4f4235f9" ] ], "meta": { @@ -21,7 +21,7 @@ "sarscov2_se_fastq_fasta_chr22_fasta - index": { "content": [ [ - "versions.yml:md5,97dfea8bc38fdb0ec800ee936e0c6e27" + "versions.yml:md5,0eaa29e412ac44532bebff0f4f4235f9" ] ], "meta": { @@ -35,53 +35,53 @@ { "0": [ [ - + ] ], "1": [ - + ], "2": [ - + ], "3": [ - + ], "4": [ [ { - + }, "null.log:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "5": [ - "versions.yml:md5,97dfea8bc38fdb0ec800ee936e0c6e27" + "versions.yml:md5,0eaa29e412ac44532bebff0f4f4235f9" ], "all_fastq": [ - + ], "index": [ [ - + ] ], "log": [ [ { - + }, "null.log:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "primary_fastq": [ - + ], "stats": [ - + ], "versions": [ - "versions.yml:md5,97dfea8bc38fdb0ec800ee936e0c6e27" + "versions.yml:md5,0eaa29e412ac44532bebff0f4f4235f9" ] } ], @@ -96,7 +96,7 @@ { "0": [ [ - + ] ], "1": [ @@ -139,7 +139,7 @@ ] ], "5": [ - "versions.yml:md5,97dfea8bc38fdb0ec800ee936e0c6e27" + "versions.yml:md5,0eaa29e412ac44532bebff0f4f4235f9" ], "all_fastq": [ [ @@ -155,7 +155,7 @@ ], "index": [ [ - + ] ], "log": [ @@ -186,7 +186,7 @@ ] ], "versions": [ - "versions.yml:md5,97dfea8bc38fdb0ec800ee936e0c6e27" + "versions.yml:md5,0eaa29e412ac44532bebff0f4f4235f9" ] } ], @@ -196,4 +196,4 @@ }, "timestamp": "2024-10-19T16:04:18.416324262" } -} \ No newline at end of file +} diff --git a/modules/nf-core/bbmap/clumpify/tests/main.nf.test.snap b/modules/nf-core/bbmap/clumpify/tests/main.nf.test.snap index e84c345f4b2..a5c8ae59a10 100644 --- a/modules/nf-core/bbmap/clumpify/tests/main.nf.test.snap +++ b/modules/nf-core/bbmap/clumpify/tests/main.nf.test.snap @@ -15,7 +15,7 @@ ], "test.clumpify.log", [ - "versions.yml:md5,fdf0404f694fca43bcf9be6458d927cd" + "versions.yml:md5,91b47f212a43c3b0072ed764c5292ebd" ] ], "meta": { @@ -37,7 +37,7 @@ ], "test.clumpify.log", [ - "versions.yml:md5,fdf0404f694fca43bcf9be6458d927cd" + "versions.yml:md5,91b47f212a43c3b0072ed764c5292ebd" ] ], "meta": { @@ -46,4 +46,4 @@ }, "timestamp": "2024-10-19T16:16:36.9005326" } -} \ No newline at end of file +} diff --git a/modules/nf-core/bbmap/filterbyname/tests/main.nf.test.snap b/modules/nf-core/bbmap/filterbyname/tests/main.nf.test.snap index 112727a5954..96ed0c028b1 100644 --- a/modules/nf-core/bbmap/filterbyname/tests/main.nf.test.snap +++ b/modules/nf-core/bbmap/filterbyname/tests/main.nf.test.snap @@ -2,7 +2,7 @@ "single end fasta": { "content": [ [ - "versions.yml:md5,4f45a3a8235bcc917fb8da60c3b537ea" + "versions.yml:md5,a5fb79be6b0878f2c78c4b4717ab3021" ] ], "meta": { @@ -14,7 +14,7 @@ "paired end fastq.bz2": { "content": [ [ - "versions.yml:md5,4f45a3a8235bcc917fb8da60c3b537ea" + "versions.yml:md5,a5fb79be6b0878f2c78c4b4717ab3021" ] ], "meta": { @@ -48,7 +48,7 @@ ] ], "2": [ - "versions.yml:md5,4f45a3a8235bcc917fb8da60c3b537ea" + "versions.yml:md5,a5fb79be6b0878f2c78c4b4717ab3021" ], "log": [ [ @@ -72,7 +72,7 @@ ] ], "versions": [ - "versions.yml:md5,4f45a3a8235bcc917fb8da60c3b537ea" + "versions.yml:md5,a5fb79be6b0878f2c78c4b4717ab3021" ] } ], @@ -85,7 +85,7 @@ "single end fastq.gz filter": { "content": [ [ - "versions.yml:md5,4f45a3a8235bcc917fb8da60c3b537ea" + "versions.yml:md5,a5fb79be6b0878f2c78c4b4717ab3021" ] ], "meta": { @@ -97,7 +97,7 @@ "single end fastq.gz - stub": { "content": [ [ - "versions.yml:md5,4f45a3a8235bcc917fb8da60c3b537ea" + "versions.yml:md5,a5fb79be6b0878f2c78c4b4717ab3021" ] ], "meta": { @@ -109,7 +109,7 @@ "paired end fastq.gz filter interleaved - stub": { "content": [ [ - "versions.yml:md5,4f45a3a8235bcc917fb8da60c3b537ea" + "versions.yml:md5,a5fb79be6b0878f2c78c4b4717ab3021" ] ], "meta": { @@ -121,7 +121,7 @@ "single end fasta - stub": { "content": [ [ - "versions.yml:md5,4f45a3a8235bcc917fb8da60c3b537ea" + "versions.yml:md5,a5fb79be6b0878f2c78c4b4717ab3021" ] ], "meta": { @@ -133,7 +133,7 @@ "paired end fastq.gz filter interleaved": { "content": [ [ - "versions.yml:md5,4f45a3a8235bcc917fb8da60c3b537ea" + "versions.yml:md5,a5fb79be6b0878f2c78c4b4717ab3021" ] ], "meta": { @@ -142,4 +142,4 @@ }, "timestamp": "2024-10-19T16:09:12.559280858" } -} \ No newline at end of file +} From 013a95c8887ae1c6b316386d84494dfbf75ef564 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Thu, 27 Feb 2025 10:27:43 +0000 Subject: [PATCH 5/6] Fix tests --- .../nf-core/bbmap/index/tests/main.nf.test.snap | 4 ++-- .../nf-core/bbmap/pileup/tests/main.nf.test.snap | 6 +++--- .../nf-core/bbmap/repair/tests/main.nf.test.snap | 14 +++++++------- .../bbmap/sendsketch/tests/main.nf.test.snap | 6 +++--- 4 files changed, 15 insertions(+), 15 deletions(-) diff --git a/modules/nf-core/bbmap/index/tests/main.nf.test.snap b/modules/nf-core/bbmap/index/tests/main.nf.test.snap index 3edd5b39563..a48ed628c19 100644 --- a/modules/nf-core/bbmap/index/tests/main.nf.test.snap +++ b/modules/nf-core/bbmap/index/tests/main.nf.test.snap @@ -12,7 +12,7 @@ [ "chr1_index_k13_c15_b1.block:md5,9f0d9a7413c1d2c16cc24555b2381163" ], - "versions.yml:md5,27981a0e7a64f63d28c9d7e27f5fde1b" + "versions.yml:md5,9caf6412abfedfdd66efd55e8f9eacc2" ], "meta": { "nf-test": "0.9.0", @@ -20,4 +20,4 @@ }, "timestamp": "2024-10-19T16:10:24.122799573" } -} \ No newline at end of file +} diff --git a/modules/nf-core/bbmap/pileup/tests/main.nf.test.snap b/modules/nf-core/bbmap/pileup/tests/main.nf.test.snap index f5e7e720d02..0e0d9467465 100644 --- a/modules/nf-core/bbmap/pileup/tests/main.nf.test.snap +++ b/modules/nf-core/bbmap/pileup/tests/main.nf.test.snap @@ -21,7 +21,7 @@ ] ], "2": [ - "versions.yml:md5,e293e3ed6387ce89f3443050f36fb079" + "versions.yml:md5,7daa294edab33a8ed9355c9eabda91c0" ], "covstats": [ [ @@ -42,7 +42,7 @@ ] ], "versions": [ - "versions.yml:md5,e293e3ed6387ce89f3443050f36fb079" + "versions.yml:md5,7daa294edab33a8ed9355c9eabda91c0" ] } ], @@ -52,4 +52,4 @@ }, "timestamp": "2024-08-26T14:33:48.464105" } -} \ No newline at end of file +} diff --git a/modules/nf-core/bbmap/repair/tests/main.nf.test.snap b/modules/nf-core/bbmap/repair/tests/main.nf.test.snap index d10edaf13aa..961d2a125fc 100644 --- a/modules/nf-core/bbmap/repair/tests/main.nf.test.snap +++ b/modules/nf-core/bbmap/repair/tests/main.nf.test.snap @@ -2,7 +2,7 @@ "sarscov2_illumina_paired - fastq_gz": { "content": [ [ - "versions.yml:md5,71de954cc3b49c64d7bd86ed82d3e892" + "versions.yml:md5,5c3df6c301609fdd4c9bc4330697bce8" ] ], "meta": { @@ -36,7 +36,7 @@ ] ], "2": [ - "versions.yml:md5,71de954cc3b49c64d7bd86ed82d3e892" + "versions.yml:md5,5c3df6c301609fdd4c9bc4330697bce8" ], "3": [ "test.repair.sh.log:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -66,7 +66,7 @@ ] ], "versions": [ - "versions.yml:md5,71de954cc3b49c64d7bd86ed82d3e892" + "versions.yml:md5,5c3df6c301609fdd4c9bc4330697bce8" ] } ], @@ -79,7 +79,7 @@ "sarscov2_illumina_interleaved - fastq_gz": { "content": [ [ - "versions.yml:md5,71de954cc3b49c64d7bd86ed82d3e892" + "versions.yml:md5,5c3df6c301609fdd4c9bc4330697bce8" ] ], "meta": { @@ -113,7 +113,7 @@ ] ], "2": [ - "versions.yml:md5,71de954cc3b49c64d7bd86ed82d3e892" + "versions.yml:md5,5c3df6c301609fdd4c9bc4330697bce8" ], "3": [ "test.repair.sh.log:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -143,7 +143,7 @@ ] ], "versions": [ - "versions.yml:md5,71de954cc3b49c64d7bd86ed82d3e892" + "versions.yml:md5,5c3df6c301609fdd4c9bc4330697bce8" ] } ], @@ -153,4 +153,4 @@ }, "timestamp": "2025-01-18T18:32:28.275703" } -} \ No newline at end of file +} diff --git a/modules/nf-core/bbmap/sendsketch/tests/main.nf.test.snap b/modules/nf-core/bbmap/sendsketch/tests/main.nf.test.snap index a8d2d31d78b..7bfdb04adab 100644 --- a/modules/nf-core/bbmap/sendsketch/tests/main.nf.test.snap +++ b/modules/nf-core/bbmap/sendsketch/tests/main.nf.test.snap @@ -9,7 +9,7 @@ "6.70%\t0.02%\t90.53%\t.\t0.34%\t4.10%\t36\t0\t9595\t2355M\t5730\tGorilla gorilla gorilla" ], [ - "versions.yml:md5,b590a08d261d92fd52e75600c1df0447" + "versions.yml:md5,d70158bc20448fb2181f0363f5dd3d3d" ] ], "meta": { @@ -28,7 +28,7 @@ "5.56%\t0.01%\t89.72%\t.\t0.12%\t5.56%\t3\t0\t9523\t29749K\t44\tPlecturocebus moloch" ], [ - "versions.yml:md5,b590a08d261d92fd52e75600c1df0447" + "versions.yml:md5,d70158bc20448fb2181f0363f5dd3d3d" ] ], "meta": { @@ -37,4 +37,4 @@ }, "timestamp": "2024-10-19T16:11:25.091320593" } -} \ No newline at end of file +} From fa797a09def84cd5e7387830460e08d805283b80 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Thu, 27 Feb 2025 10:38:11 +0000 Subject: [PATCH 6/6] Fix singularity uris --- modules/nf-core/bbmap/bbduk/main.nf | 2 +- modules/nf-core/bbmap/bbmerge/main.nf | 2 +- modules/nf-core/bbmap/bbsplit/main.nf | 2 +- modules/nf-core/bbmap/clumpify/main.nf | 2 +- modules/nf-core/bbmap/filterbyname/main.nf | 2 +- modules/nf-core/bbmap/index/main.nf | 2 +- modules/nf-core/bbmap/repair/main.nf | 2 +- modules/nf-core/bbmap/sendsketch/main.nf | 2 +- 8 files changed, 8 insertions(+), 8 deletions(-) diff --git a/modules/nf-core/bbmap/bbduk/main.nf b/modules/nf-core/bbmap/bbduk/main.nf index 58a598bb1f5..5a945a3c10c 100644 --- a/modules/nf-core/bbmap/bbduk/main.nf +++ b/modules/nf-core/bbmap/bbduk/main.nf @@ -4,7 +4,7 @@ process BBMAP_BBDUK { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bbmap:39.17--h44cf5ac_0': + 'https://depot.galaxyproject.org/singularity/bbmap:39.17--he5f24ec_0': 'biocontainers/bbmap:39.17--he5f24ec_0' }" input: diff --git a/modules/nf-core/bbmap/bbmerge/main.nf b/modules/nf-core/bbmap/bbmerge/main.nf index 52374b62e4c..b815e76552a 100644 --- a/modules/nf-core/bbmap/bbmerge/main.nf +++ b/modules/nf-core/bbmap/bbmerge/main.nf @@ -3,7 +3,7 @@ process BBMAP_BBMERGE { label 'process_single' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bbmap:39.17--h44cf5ac_0': + 'https://depot.galaxyproject.org/singularity/bbmap:39.17--he5f24ec_0': 'biocontainers/bbmap:39.17--he5f24ec_0' }" input: diff --git a/modules/nf-core/bbmap/bbsplit/main.nf b/modules/nf-core/bbmap/bbsplit/main.nf index 9e85cd78710..99c18eaa539 100644 --- a/modules/nf-core/bbmap/bbsplit/main.nf +++ b/modules/nf-core/bbmap/bbsplit/main.nf @@ -5,7 +5,7 @@ process BBMAP_BBSPLIT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bbmap:39.17--h44cf5ac_0': + 'https://depot.galaxyproject.org/singularity/bbmap:39.17--he5f24ec_0': 'biocontainers/bbmap:39.17--he5f24ec_0' }" input: diff --git a/modules/nf-core/bbmap/clumpify/main.nf b/modules/nf-core/bbmap/clumpify/main.nf index 59df170e255..a11a82ab059 100644 --- a/modules/nf-core/bbmap/clumpify/main.nf +++ b/modules/nf-core/bbmap/clumpify/main.nf @@ -5,7 +5,7 @@ process BBMAP_CLUMPIFY { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bbmap:39.17--h44cf5ac_0': + 'https://depot.galaxyproject.org/singularity/bbmap:39.17--he5f24ec_0': 'biocontainers/bbmap:39.17--he5f24ec_0' }" input: diff --git a/modules/nf-core/bbmap/filterbyname/main.nf b/modules/nf-core/bbmap/filterbyname/main.nf index 8612ff3f85d..301fe36f706 100644 --- a/modules/nf-core/bbmap/filterbyname/main.nf +++ b/modules/nf-core/bbmap/filterbyname/main.nf @@ -4,7 +4,7 @@ process BBMAP_FILTERBYNAME { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bbmap:39.17--h44cf5ac_0': + 'https://depot.galaxyproject.org/singularity/bbmap:39.17--he5f24ec_0': 'biocontainers/bbmap:39.17--he5f24ec_0' }" input: diff --git a/modules/nf-core/bbmap/index/main.nf b/modules/nf-core/bbmap/index/main.nf index 7ab3a412c3a..e90ac824579 100644 --- a/modules/nf-core/bbmap/index/main.nf +++ b/modules/nf-core/bbmap/index/main.nf @@ -4,7 +4,7 @@ process BBMAP_INDEX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bbmap:39.17--h44cf5ac_0': + 'https://depot.galaxyproject.org/singularity/bbmap:39.17--he5f24ec_0': 'biocontainers/bbmap:39.17--he5f24ec_0' }" input: diff --git a/modules/nf-core/bbmap/repair/main.nf b/modules/nf-core/bbmap/repair/main.nf index 41845d85690..d97474b3965 100644 --- a/modules/nf-core/bbmap/repair/main.nf +++ b/modules/nf-core/bbmap/repair/main.nf @@ -3,7 +3,7 @@ process BBMAP_REPAIR { label 'process_single' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bbmap:39.17--h44cf5ac_0': + 'https://depot.galaxyproject.org/singularity/bbmap:39.17--he5f24ec_0': 'biocontainers/bbmap:39.17--he5f24ec_0' }" input: diff --git a/modules/nf-core/bbmap/sendsketch/main.nf b/modules/nf-core/bbmap/sendsketch/main.nf index 27664545054..0cb1bddb197 100644 --- a/modules/nf-core/bbmap/sendsketch/main.nf +++ b/modules/nf-core/bbmap/sendsketch/main.nf @@ -4,7 +4,7 @@ process BBMAP_SENDSKETCH { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bbmap:39.17--h44cf5ac_0': + 'https://depot.galaxyproject.org/singularity/bbmap:39.17--he5f24ec_0': 'biocontainers/bbmap:39.17--he5f24ec_0' }" input: