fix bug for non standard fastq file

y9c · Jul 29, 2023 · 7202325 · 7202325
1 parent 28d84f8
commit 7202325
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/Snakefile b/Snakefile
@@ -203,14 +203,14 @@ rule run_cutadapt:
             SAMPLE2BARCODE[wildcards.sample]["umi5"],
             SAMPLE2BARCODE[wildcards.sample]["umi3"],
         )
-        + ' --rename="{id}_{cut_prefix}{cut_suffix} {comment}"'
+        + ' --rename="{id}_{cut_prefix}{cut_suffix}"'
         if SAMPLE2BARCODE[wildcards.sample]["umi5"] > 0
         and SAMPLE2BARCODE[wildcards.sample]["umi3"] > 0
         else "-u {}".format(SAMPLE2BARCODE[wildcards.sample]["umi5"])
-        + ' --rename="{id}_{cut_prefix} {comment}"'
+        + ' --rename="{id}_{cut_prefix}"'
         if SAMPLE2BARCODE[wildcards.sample]["umi5"] > 0
         else "-u -{}".format(SAMPLE2BARCODE[wildcards.sample]["umi3"])
-        + ' --rename="{id}_{cut_suffix} {comment}"'
+        + ' --rename="{id}_{cut_suffix}"'
         if SAMPLE2BARCODE[wildcards.sample]["umi3"] > 0
         else "",
         mask_ends_args=lambda wildcards: "-u {}".format(

diff --git a/bin/joinFastq b/bin/joinFastq