diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 8df4c5e..d16ed7e 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -21,6 +21,7 @@ run_modules: - bowtie2 - kraken - malt + - custom_content #extra_fn_clean_exts: # - '_fastp' diff --git a/conf/modules.config b/conf/modules.config index 0330abb..1f4914d 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -241,7 +241,8 @@ process { withName: PRINSEQPLUSPLUS { ext.args = [ 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() ext.prefix = { "${meta.id}-${meta.run_accession}" } publishDir = [