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Update nextflow.config #1211

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merged 2 commits into from
Nov 16, 2021
Merged

Update nextflow.config #1211

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08008d3
Update nextflow.config
maxulysse Jul 16, 2021
b35d1f2
Merge branch 'master' into maxulysse-patch-2
ewels Nov 16, 2021
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14 changes: 7 additions & 7 deletions nf_core/pipeline-template/nextflow.config
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Original file line number Diff line number Diff line change
Expand Up @@ -67,13 +67,6 @@ try {
System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
}

// Load igenomes.config if required
if (!params.igenomes_ignore) {
includeConfig 'conf/igenomes.config'
} else {
params.genomes = [:]
}

profiles {
debug { process.beforeScript = 'echo $HOSTNAME' }
conda {
Expand Down Expand Up @@ -125,6 +118,13 @@ profiles {
test_full { includeConfig 'conf/test_full.config' }
}

// Load igenomes.config if required
if (!params.igenomes_ignore) {
includeConfig 'conf/igenomes.config'
} else {
params.genomes = [:]
}

// Export these variables to prevent local Python/R libraries from conflicting with those in the container
env {
PYTHONNOUSERSITE = 1
Expand Down