From e1da721a9371aa501119208125bf75c70c8a9c2e Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Fri, 8 Mar 2024 10:38:03 -0500 Subject: [PATCH] bump igblast versions --- modules/local/changeo/changeo_assigngenes.nf | 2 +- modules/local/changeo/changeo_convertdb_fasta.nf | 2 +- modules/local/changeo/changeo_creategermlines.nf | 2 +- modules/local/changeo/changeo_makedb.nf | 3 ++- modules/local/changeo/changeo_parsedb_select.nf | 2 +- modules/local/changeo/changeo_parsedb_split.nf | 2 +- modules/local/fetch_databases.nf | 2 +- modules/local/gunzip.nf | 2 +- modules/local/unzip_db.nf | 2 +- 9 files changed, 10 insertions(+), 9 deletions(-) diff --git a/modules/local/changeo/changeo_assigngenes.nf b/modules/local/changeo/changeo_assigngenes.nf index a51331cf..bbc1afec 100644 --- a/modules/local/changeo/changeo_assigngenes.nf +++ b/modules/local/changeo/changeo_assigngenes.nf @@ -3,7 +3,7 @@ process CHANGEO_ASSIGNGENES { label 'process_low' label 'immcantation' - conda "bioconda::changeo=1.3.0 bioconda::igblast=1.19.0 conda-forge::wget=1.20.1" + conda "bioconda::changeo=1.3.0 bioconda::igblast=1.22.0 conda-forge::wget=1.20.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-7d8e418eb73acc6a80daea8e111c94cf19a4ecfd:00534555924705cdf2f7ac48b4b8b4083527ca58-1' : 'biocontainers/mulled-v2-7d8e418eb73acc6a80daea8e111c94cf19a4ecfd:00534555924705cdf2f7ac48b4b8b4083527ca58-1' }" diff --git a/modules/local/changeo/changeo_convertdb_fasta.nf b/modules/local/changeo/changeo_convertdb_fasta.nf index 99355f33..58b1c214 100644 --- a/modules/local/changeo/changeo_convertdb_fasta.nf +++ b/modules/local/changeo/changeo_convertdb_fasta.nf @@ -4,7 +4,7 @@ process CHANGEO_CONVERTDB_FASTA { label 'immcantation' - conda "bioconda::changeo=1.3.0 bioconda::igblast=1.19.0 conda-forge::wget=1.20.1" + conda "bioconda::changeo=1.3.0 bioconda::igblast=1.22.0 conda-forge::wget=1.20.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-7d8e418eb73acc6a80daea8e111c94cf19a4ecfd:00534555924705cdf2f7ac48b4b8b4083527ca58-1' : 'biocontainers/mulled-v2-7d8e418eb73acc6a80daea8e111c94cf19a4ecfd:00534555924705cdf2f7ac48b4b8b4083527ca58-1' }" diff --git a/modules/local/changeo/changeo_creategermlines.nf b/modules/local/changeo/changeo_creategermlines.nf index feef1d2b..f0d5efa3 100644 --- a/modules/local/changeo/changeo_creategermlines.nf +++ b/modules/local/changeo/changeo_creategermlines.nf @@ -4,7 +4,7 @@ process CHANGEO_CREATEGERMLINES { label 'immcantation' - conda "bioconda::changeo=1.3.0 bioconda::igblast=1.19.0 conda-forge::wget=1.20.1" + conda "bioconda::changeo=1.3.0 bioconda::igblast=1.22.0 conda-forge::wget=1.20.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-7d8e418eb73acc6a80daea8e111c94cf19a4ecfd:00534555924705cdf2f7ac48b4b8b4083527ca58-1' : 'biocontainers/mulled-v2-7d8e418eb73acc6a80daea8e111c94cf19a4ecfd:00534555924705cdf2f7ac48b4b8b4083527ca58-1' }" diff --git a/modules/local/changeo/changeo_makedb.nf b/modules/local/changeo/changeo_makedb.nf index e392cda9..00f2b7d3 100644 --- a/modules/local/changeo/changeo_makedb.nf +++ b/modules/local/changeo/changeo_makedb.nf @@ -4,8 +4,9 @@ process CHANGEO_MAKEDB { label 'immcantation' - conda "bioconda::changeo=1.3.0 bioconda::igblast=1.19.0 conda-forge::wget=1.20.1" + conda "bioconda::changeo=1.3.0 bioconda::igblast=1.22.0 conda-forge::wget=1.20.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + //TODO: update mulled containers when available 'https://depot.galaxyproject.org/singularity/mulled-v2-7d8e418eb73acc6a80daea8e111c94cf19a4ecfd:00534555924705cdf2f7ac48b4b8b4083527ca58-1' : 'biocontainers/mulled-v2-7d8e418eb73acc6a80daea8e111c94cf19a4ecfd:00534555924705cdf2f7ac48b4b8b4083527ca58-1' }" diff --git a/modules/local/changeo/changeo_parsedb_select.nf b/modules/local/changeo/changeo_parsedb_select.nf index 9f592e7f..afb3fa64 100644 --- a/modules/local/changeo/changeo_parsedb_select.nf +++ b/modules/local/changeo/changeo_parsedb_select.nf @@ -4,7 +4,7 @@ process CHANGEO_PARSEDB_SELECT { label 'immcantation' - conda "bioconda::changeo=1.3.0 bioconda::igblast=1.19.0 conda-forge::wget=1.20.1" + conda "bioconda::changeo=1.3.0 bioconda::igblast=1.22.0 conda-forge::wget=1.20.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-7d8e418eb73acc6a80daea8e111c94cf19a4ecfd:00534555924705cdf2f7ac48b4b8b4083527ca58-1' : 'biocontainers/mulled-v2-7d8e418eb73acc6a80daea8e111c94cf19a4ecfd:00534555924705cdf2f7ac48b4b8b4083527ca58-1' }" diff --git a/modules/local/changeo/changeo_parsedb_split.nf b/modules/local/changeo/changeo_parsedb_split.nf index 354c3019..5c581662 100644 --- a/modules/local/changeo/changeo_parsedb_split.nf +++ b/modules/local/changeo/changeo_parsedb_split.nf @@ -4,7 +4,7 @@ process CHANGEO_PARSEDB_SPLIT { label 'immcantation' - conda "bioconda::changeo=1.3.0 bioconda::igblast=1.19.0 conda-forge::wget=1.20.1" + conda "bioconda::changeo=1.3.0 bioconda::igblast=1.22.0 conda-forge::wget=1.20.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-7d8e418eb73acc6a80daea8e111c94cf19a4ecfd:00534555924705cdf2f7ac48b4b8b4083527ca58-1' : 'biocontainers/mulled-v2-7d8e418eb73acc6a80daea8e111c94cf19a4ecfd:00534555924705cdf2f7ac48b4b8b4083527ca58-1' }" diff --git a/modules/local/fetch_databases.nf b/modules/local/fetch_databases.nf index b1d10ea3..d489d10e 100644 --- a/modules/local/fetch_databases.nf +++ b/modules/local/fetch_databases.nf @@ -3,7 +3,7 @@ process FETCH_DATABASES { label 'process_low' label 'immcantation' - conda "bioconda::changeo=1.3.0 bioconda::igblast=1.19.0 conda-forge::wget=1.20.1" + conda "bioconda::changeo=1.3.0 bioconda::igblast=1.22.0 conda-forge::wget=1.20.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-7d8e418eb73acc6a80daea8e111c94cf19a4ecfd:00534555924705cdf2f7ac48b4b8b4083527ca58-1' : 'biocontainers/mulled-v2-7d8e418eb73acc6a80daea8e111c94cf19a4ecfd:00534555924705cdf2f7ac48b4b8b4083527ca58-1' }" diff --git a/modules/local/gunzip.nf b/modules/local/gunzip.nf index 3d0e2fb8..2a929579 100644 --- a/modules/local/gunzip.nf +++ b/modules/local/gunzip.nf @@ -5,7 +5,7 @@ process GUNZIP { conda "conda-forge::sed=4.7" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' : - 'docker.io/biocontainers/biocontainers:v1.2.0_cv1' }" + 'biocontainers/biocontainers:v1.2.0_cv1' }" input: tuple val(meta), path(R1), path(R2) diff --git a/modules/local/unzip_db.nf b/modules/local/unzip_db.nf index 3f78313c..10f49619 100644 --- a/modules/local/unzip_db.nf +++ b/modules/local/unzip_db.nf @@ -5,7 +5,7 @@ process UNZIP_DB { conda "conda-forge::sed=4.7" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' : - 'docker.io/biocontainers/biocontainers:v1.2.0_cv1' }" + 'biocontainers/biocontainers:v1.2.0_cv1' }" input: path(archive)