diff --git a/config/config.yaml b/config/config.yaml index 2279843..804c358 100644 --- a/config/config.yaml +++ b/config/config.yaml @@ -22,7 +22,6 @@ data: preproc: activate: true # whether (=true) or not (=false) to include pre-processing minlen: 10 - qual: 20 slidingwindow: activate: true wsize: 3 diff --git a/workflow/rules/preproc.smk b/workflow/rules/preproc.smk index 849372e..0c8e4b0 100644 --- a/workflow/rules/preproc.smk +++ b/workflow/rules/preproc.smk @@ -82,7 +82,7 @@ rule preproc_paired_end: params: dapters="", extra=lambda wildcards: "-u 100 -e {0} -l {1} {2} ".format( - config['preproc']['qual'], + config['basequal'], config['preproc']['minlen'], "-3 --cut_tail_window_size {} cut_tail_mean_quality {}".format( config['preproc']['slidingwindow']['wsize'],