From 264ac253821b64276bcf998ac0e766b73a36619f Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 16 Aug 2024 18:08:38 +0200 Subject: [PATCH] use quay.io for all containers --- modules/local/arriba/download/main.nf | 2 +- modules/local/convert2bed/main.nf | 2 +- modules/local/ensembl/main.nf | 2 +- modules/local/fusioncatcher/detect/main.nf | 2 +- modules/local/fusioncatcher/download/main.nf | 2 +- modules/local/fusioninspector/main.nf | 2 +- modules/local/fusionreport/detect/main.nf | 3 +-- modules/local/fusionreport/download/main.nf | 2 +- modules/local/hgnc/main.nf | 2 +- modules/local/rrnatranscripts/main.nf | 3 +-- modules/local/starfusion/build/main.nf | 2 +- modules/local/starfusion/detect/main.nf | 2 +- modules/local/starfusion/download/main.nf | 2 +- modules/local/uscs/custom_gtftogenepred/main.nf | 2 +- modules/local/vcf_collect/main.nf | 2 +- 15 files changed, 15 insertions(+), 17 deletions(-) diff --git a/modules/local/arriba/download/main.nf b/modules/local/arriba/download/main.nf index 61b9a91f..d4e33cec 100644 --- a/modules/local/arriba/download/main.nf +++ b/modules/local/arriba/download/main.nf @@ -5,7 +5,7 @@ process ARRIBA_DOWNLOAD { conda "bioconda::gnu-wget=1.18" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gnu-wget:1.18--h5bf99c6_5' : - 'quay.io/biocontainers/gnu-wget:1.18--h5bf99c6_5' }" + 'biocontainers/gnu-wget:1.18--h5bf99c6_5' }" output: path "versions.yml" , emit: versions diff --git a/modules/local/convert2bed/main.nf b/modules/local/convert2bed/main.nf index c4313f0a..7aafd779 100644 --- a/modules/local/convert2bed/main.nf +++ b/modules/local/convert2bed/main.nf @@ -5,7 +5,7 @@ process CONVERT2BED { conda "bioconda::bedops=2.4.41" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bedops:2.4.41--h9f5acd7_0' : - 'quay.io/biocontainers/bedops:2.4.41--h9f5acd7_0' }" + 'biocontainers/bedops:2.4.41--h9f5acd7_0' }" input: tuple val(meta), path(gtf) diff --git a/modules/local/ensembl/main.nf b/modules/local/ensembl/main.nf index 8297e290..2d1be710 100644 --- a/modules/local/ensembl/main.nf +++ b/modules/local/ensembl/main.nf @@ -5,7 +5,7 @@ process ENSEMBL_DOWNLOAD { conda "bioconda::gnu-wget=1.18" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gnu-wget:1.18--h5bf99c6_5' : - 'quay.io/biocontainers/gnu-wget:1.18--h5bf99c6_5' }" + 'biocontainers/gnu-wget:1.18--h5bf99c6_5' }" input: val ensembl_version diff --git a/modules/local/fusioncatcher/detect/main.nf b/modules/local/fusioncatcher/detect/main.nf index 2977d668..30e641db 100644 --- a/modules/local/fusioncatcher/detect/main.nf +++ b/modules/local/fusioncatcher/detect/main.nf @@ -3,7 +3,7 @@ process FUSIONCATCHER { label 'process_high' conda "bioconda::fusioncatcher=1.33" - container "docker.io/clinicalgenomics/fusioncatcher:1.33" + container "nf-core/fusioncatcher:1.33" input: tuple val(meta), path(fasta) diff --git a/modules/local/fusioncatcher/download/main.nf b/modules/local/fusioncatcher/download/main.nf index 156e70b6..0f9178c8 100644 --- a/modules/local/fusioncatcher/download/main.nf +++ b/modules/local/fusioncatcher/download/main.nf @@ -3,7 +3,7 @@ process FUSIONCATCHER_DOWNLOAD { label 'process_medium' conda "bioconda::fusioncatcher=1.33" - container "docker.io/clinicalgenomics/fusioncatcher:1.33" + container "nf-core/fusioncatcher:1.33" output: path "*" , emit: reference diff --git a/modules/local/fusioninspector/main.nf b/modules/local/fusioninspector/main.nf index c7fcd3f0..068e4931 100644 --- a/modules/local/fusioninspector/main.nf +++ b/modules/local/fusioninspector/main.nf @@ -3,7 +3,7 @@ process FUSIONINSPECTOR { label 'process_high' conda "bioconda::dfam=3.3 bioconda::hmmer=3.3.2 bioconda::star-fusion=1.12.0 bioconda::samtools=1.9 bioconda::star=2.7.8a" - container 'docker.io/trinityctat/starfusion:1.12.0' + container "nf-core/starfusion:1.12.0" input: tuple val(meta), path(reads), path(fusion_list) diff --git a/modules/local/fusionreport/detect/main.nf b/modules/local/fusionreport/detect/main.nf index 8024d8f8..46b289b1 100644 --- a/modules/local/fusionreport/detect/main.nf +++ b/modules/local/fusionreport/detect/main.nf @@ -3,8 +3,7 @@ process FUSIONREPORT { label 'process_medium' conda "bioconda::star=2.7.9a" - container "docker.io/clinicalgenomics/fusion-report:2.1.8" - + container "nf-core/fusion-report:2.1.8" input: tuple val(meta), path(reads), path(arriba_fusions), path(starfusion_fusions), path(fusioncatcher_fusions) diff --git a/modules/local/fusionreport/download/main.nf b/modules/local/fusionreport/download/main.nf index ac288ade..3d08360c 100644 --- a/modules/local/fusionreport/download/main.nf +++ b/modules/local/fusionreport/download/main.nf @@ -3,7 +3,7 @@ process FUSIONREPORT_DOWNLOAD { label 'process_medium' conda "bioconda::star=2.7.9a" - container "docker.io/clinicalgenomics/fusion-report:2.1.8" + container "nf-core/fusion-report:2.1.8" input: val(username) diff --git a/modules/local/hgnc/main.nf b/modules/local/hgnc/main.nf index 1b3808f6..500fe8a6 100644 --- a/modules/local/hgnc/main.nf +++ b/modules/local/hgnc/main.nf @@ -5,7 +5,7 @@ process HGNC_DOWNLOAD { conda "bioconda::gnu-wget=1.18" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gnu-wget:1.18--h5bf99c6_5' : - 'quay.io/biocontainers/gnu-wget:1.18--h5bf99c6_5' }" + 'biocontainers/gnu-wget:1.18--h5bf99c6_5' }" input: diff --git a/modules/local/rrnatranscripts/main.nf b/modules/local/rrnatranscripts/main.nf index e4afc284..8055f955 100644 --- a/modules/local/rrnatranscripts/main.nf +++ b/modules/local/rrnatranscripts/main.nf @@ -6,8 +6,7 @@ process RRNA_TRANSCRIPTS { container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/python:3.9--1' : - 'quay.io/biocontainers/python:3.9--1' }" - + 'biocontainers/python:3.9--1' }" input: tuple val(meta), path(gtf) diff --git a/modules/local/starfusion/build/main.nf b/modules/local/starfusion/build/main.nf index e2bd7879..b6043df8 100644 --- a/modules/local/starfusion/build/main.nf +++ b/modules/local/starfusion/build/main.nf @@ -2,7 +2,7 @@ process STARFUSION_BUILD { tag 'star-fusion' conda "bioconda::dfam=3.3 bioconda::hmmer=3.3.2 bioconda::star-fusion=1.12.0 bioconda::trinity=2.13.2 bioconda::samtools=1.9 bioconda::star=2.7.8a" - container "docker.io/trinityctat/starfusion:1.12.0" + container "nf-core/starfusion:1.12.0" input: tuple val(meta), path(fasta) diff --git a/modules/local/starfusion/detect/main.nf b/modules/local/starfusion/detect/main.nf index 1994d555..35f21dd9 100644 --- a/modules/local/starfusion/detect/main.nf +++ b/modules/local/starfusion/detect/main.nf @@ -3,7 +3,7 @@ process STARFUSION { label 'process_high' conda "bioconda::dfam=3.3 bioconda::hmmer=3.3.2 bioconda::star-fusion=1.12.0 bioconda::trinity=2.13.2 bioconda::samtools=1.9 bioconda::star=2.7.8a" - container 'docker.io/trinityctat/starfusion:1.12.0' + container "nf-core/starfusion:1.12.0" input: tuple val(meta), path(reads), path(junction) diff --git a/modules/local/starfusion/download/main.nf b/modules/local/starfusion/download/main.nf index 9c9b1482..12294fb8 100644 --- a/modules/local/starfusion/download/main.nf +++ b/modules/local/starfusion/download/main.nf @@ -2,7 +2,7 @@ process STARFUSION_DOWNLOAD { tag 'star-fusion' conda "bioconda::dfam=3.3 bioconda::hmmer=3.3.2 bioconda::star-fusion=1.12.0 bioconda::trinity=2.13.2 bioconda::samtools=1.9 bioconda::star=2.7.8a" - container 'docker.io/trinityctat/starfusion:1.12.0' + container "nf-core/starfusion:1.12.0" output: path "ctat_genome_lib_build_dir/*" , emit: reference diff --git a/modules/local/uscs/custom_gtftogenepred/main.nf b/modules/local/uscs/custom_gtftogenepred/main.nf index 78fcbd29..562e854b 100644 --- a/modules/local/uscs/custom_gtftogenepred/main.nf +++ b/modules/local/uscs/custom_gtftogenepred/main.nf @@ -4,7 +4,7 @@ process GTF_TO_REFFLAT { conda "bioconda::ucsc-gtftogenepred=377" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ucsc-gtftogenepred:377--ha8a8165_5' : - 'quay.io/biocontainers/ucsc-gtftogenepred:377--ha8a8165_5' }" + 'biocontainers/ucsc-gtftogenepred:377--ha8a8165_5' }" input: tuple val(meta), path (gtf) diff --git a/modules/local/vcf_collect/main.nf b/modules/local/vcf_collect/main.nf index 3ede7936..3a1bf221 100644 --- a/modules/local/vcf_collect/main.nf +++ b/modules/local/vcf_collect/main.nf @@ -5,7 +5,7 @@ process VCF_COLLECT { conda "conda-forge::pandas=1.5.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pandas:1.5.2' : - 'quay.io/biocontainers/pandas:1.5.2' }" + 'biocontainers/pandas:1.5.2' }" input: tuple val(meta), path(fusioninspector_tsv), path(fusioninspector_gtf_tsv), path(fusionreport_report), path(fusionreport_csv)