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Code Issues Releases Packages Activity

add missing parameters to nextflow.config

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This commit is contained in:
Mahwash Jamy 2022-10-31 16:07:53 +00:00
parent 3147a80a56
commit febcbfc057
2 changed files with 7 additions and 1 deletions
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3
conf/modules.config
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@ -335,7 +335,8 @@ process {
withName: KRAKENUNIQ_PRELOADEDKRAKENUNIQ { withName: KRAKENUNIQ_PRELOADEDKRAKENUNIQ {
ext.args = { "${meta.db_params}" } ext.args = { "${meta.db_params}" }
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" } // one run with multiple samples, so fix ID to just db name to ensure clean log name
ext.prefix = { "${meta.db_name}" }
publishDir = [ publishDir = [
path: { "${params.outdir}/krakenuniq/${meta.db_name}/" }, path: { "${params.outdir}/krakenuniq/${meta.db_name}/" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,

5
nextflow.config
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@ -118,6 +118,11 @@ params {
kraken2_save_readclassification = false // added directly to module in profiling.nf kraken2_save_readclassification = false // added directly to module in profiling.nf
kraken2_save_minimizers = false kraken2_save_minimizers = false
//krakenuniq
run_krakenuniq = false
krakenuniq_save_reads = false // added directly to module in profiling.nf
krakenuniq_save_readclassifications = false // added directly to module in profiling.nf
// Bracken // Bracken
run_bracken = false run_bracken = false