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Use quay.io as registry for all containers #497

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Use quay.io as registry for all containers #497

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2 changes: 1 addition & 1 deletion modules/local/arriba/download/main.nf
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion modules/local/convert2bed/main.nf
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Expand Up @@ -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)
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2 changes: 1 addition & 1 deletion modules/local/ensembl/main.nf
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion modules/local/fusioncatcher/detect/main.nf
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Expand Up @@ -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)
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2 changes: 1 addition & 1 deletion modules/local/fusioncatcher/download/main.nf
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion modules/local/fusioninspector/main.nf
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Expand Up @@ -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)
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3 changes: 1 addition & 2 deletions modules/local/fusionreport/detect/main.nf
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Expand Up @@ -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)
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2 changes: 1 addition & 1 deletion modules/local/fusionreport/download/main.nf
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Expand Up @@ -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)
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2 changes: 1 addition & 1 deletion modules/local/hgnc/main.nf
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Expand Up @@ -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:

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3 changes: 1 addition & 2 deletions modules/local/rrnatranscripts/main.nf
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Expand Up @@ -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)
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2 changes: 1 addition & 1 deletion modules/local/starfusion/build/main.nf
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Expand Up @@ -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)
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2 changes: 1 addition & 1 deletion modules/local/starfusion/detect/main.nf
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Expand Up @@ -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)
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2 changes: 1 addition & 1 deletion modules/local/starfusion/download/main.nf
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion modules/local/uscs/custom_gtftogenepred/main.nf
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Expand Up @@ -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)
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2 changes: 1 addition & 1 deletion modules/local/vcf_collect/main.nf
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Expand Up @@ -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)
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