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This commit is contained in:
James Fellows Yates 2022-08-23 14:24:57 +02:00
parent de70b0a01d
commit a97bb69cd2
2 changed files with 3 additions and 1 deletions
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1
assets/multiqc_config.yml
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@ -21,6 +21,7 @@ run_modules:
- bowtie2 - bowtie2
- kraken - kraken
- malt - malt
- custom_content
#extra_fn_clean_exts: #extra_fn_clean_exts:
# - '_fastp' # - '_fastp'

3
conf/modules.config
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@ -241,7 +241,8 @@ process {
withName: PRINSEQPLUSPLUS { withName: PRINSEQPLUSPLUS {
ext.args = [ ext.args = [
params.shortread_complexityfilter_prinseqplusplus_mode == 'dust' ? "-lc_dust=${params.shortread_complexityfilter_prinseqplusplus_dustscore}" : "-lc_entropy=${params.shortread_complexityfilter_entropy}", params.shortread_complexityfilter_prinseqplusplus_mode == 'dust' ? "-lc_dust=${params.shortread_complexityfilter_prinseqplusplus_dustscore}" : "-lc_entropy=${params.shortread_complexityfilter_entropy}",
"-trim_qual_left=0 -trim_qual_left=0 -trim_qual_window=0 -trim_qual_step=0" "-trim_qual_left=0 -trim_qual_left=0 -trim_qual_window=0 -trim_qual_step=0",
"-VERBOSE 2"
].join(' ').trim() ].join(' ').trim()
ext.prefix = { "${meta.id}-${meta.run_accession}" } ext.prefix = { "${meta.id}-${meta.run_accession}" }
publishDir = [ publishDir = [