removed local base quality parameter in preproc

ylab-hi · Jan 16, 2024 · a96cf91 · a96cf91
1 parent b82dfb9
commit a96cf91
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Showing 2 changed files with 1 addition and 2 deletions.
diff --git 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
@@ -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'],