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2 changed files with 3 additions and 1 deletions
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@ -21,6 +21,7 @@ run_modules:
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- bowtie2
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- kraken
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- malt
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- custom_content
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#extra_fn_clean_exts:
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# - '_fastp'
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@ -241,7 +241,8 @@ process {
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withName: PRINSEQPLUSPLUS {
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ext.args = [
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params.shortread_complexityfilter_prinseqplusplus_mode == 'dust' ? "-lc_dust=${params.shortread_complexityfilter_prinseqplusplus_dustscore}" : "-lc_entropy=${params.shortread_complexityfilter_entropy}",
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"-trim_qual_left=0 -trim_qual_left=0 -trim_qual_window=0 -trim_qual_step=0"
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"-trim_qual_left=0 -trim_qual_left=0 -trim_qual_window=0 -trim_qual_step=0",
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"-VERBOSE 2"
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].join(' ').trim()
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ext.prefix = { "${meta.id}-${meta.run_accession}" }
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publishDir = [
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