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nextflow.config

Lines changed: 17 additions & 27 deletions
Original file line numberDiff line numberDiff line change
@@ -175,16 +175,8 @@ profiles {
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test_vep { includeConfig 'conf/test_vep.config' }
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}
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// Load nf-core custom profiles from different institutions
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// If params.custom_config_base is set AND either the NXF_OFFLINE environment variable is not set or params.custom_config_base is a local path, the nfcore_custom.config file from the specified base path is included.
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// Load qbic-pipelines/vcftomaf custom profiles from different institutions.
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includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
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// Load qbic-pipelines/vcftomaf custom profiles from different institutions.
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// TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
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// includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/pipeline/vcftomaf.config" : "/dev/null"
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includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/pipeline/vcftomaf.config" : "/dev/null"
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// Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
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// Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled
@@ -198,7 +190,6 @@ charliecloud.registry = 'quay.io'
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// Load nf-core custom profiles from different Institutions
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includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
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// Load igenomes.config if required
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includeConfig !params.igenomes_ignore ? 'conf/igenomes.config' : 'conf/igenomes_ignored.config'
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@@ -246,30 +237,29 @@ dag {
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manifest {
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name = 'qbic-pipelines/vcftomaf'
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contributors = [
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// TODO nf-core: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
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[
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name: 'SusiJo',
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affiliation: '',
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name: 'Susanne Jodoin',
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affiliation: 'Quantitative Biology Center (QBiC) Tübingen, University of Tübingen, Germany',
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email: '',
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github: '',
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contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor')
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orcid: ''
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github: '@SusiJo',
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contribution: ['author'],
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orcid: '0009-0001-9152-7291'
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],
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[
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name: ' FriederikeHanssen',
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affiliation: '',
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name: 'Friederike Hanssen',
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affiliation: 'Seqera',
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email: '',
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github: '',
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contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor')
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orcid: ''
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github: '@FriederikeHanssen',
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contribution: ['author'],
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orcid: '0009-0001-9875-5262'
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],
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[
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name: ' famosab',
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affiliation: '',
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email: '',
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github: '',
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contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor')
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orcid: ''
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name: 'Famke Bäuerle',
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affiliation: 'Quantitative Biology Center (QBiC) Tübingen, University of Tübingen, Germany',
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email: 'famke.baeuerle@uni-tuebingen.de',
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github: '@famosab',
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contribution: ['maintainer'],
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orcid: '0000-0003-1387-0251'
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],
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]
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homePage = 'https://github.com/qbic-pipelines/vcftomaf'

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