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conf
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nextflow.config

Lines changed: 2 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -174,9 +174,6 @@ profiles {
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test { includeConfig 'conf/test.config' }
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}
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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')) ? "${params.custom_config_base}/pipeline/vcftomaf.config" : "/dev/null"
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// Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
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// Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled
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// Set to your registry if you have a mirror of containers
@@ -186,16 +183,15 @@ podman.registry = 'quay.io'
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singularity.registry = 'quay.io'
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charliecloud.registry = 'quay.io'
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// Load nf-core custom profiles from different institutions
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includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE')|| !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
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// Load nf-core 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 igenomes.config if required
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includeConfig !params.igenomes_ignore ? 'conf/igenomes.config' : 'conf/igenomes_ignored.config'
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// Export these variables to prevent local Python/R libraries from conflicting with those in the container
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// The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
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// See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.
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env {
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PYTHONNOUSERSITE = 1
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R_PROFILE_USER = "/.Rprofile"

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