Fix typo in bbmap count summary output filename

ctmrbio · Aug 30, 2021 · c75bcb8 · c75bcb8
1 parent 0cf7b7a
commit c75bcb8
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Showing 2 changed files with 3 additions and 2 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -29,6 +29,7 @@ situations.
 - `preprocessing_summary.py` now parses the correct number of unclassified reads.
 - Rule `bracken_kreport` now correctly produces kreport output file for
   downstream processing.
+- Fixed typo in count summary output filenames for BBMap.
 
 ### Changed
 

diff --git a/rules/mappers/bbmap.smk b/rules/mappers/bbmap.smk
@@ -23,7 +23,7 @@ for bbmap_config in config["bbmap"]:
                 db_name=bbmap_config["db_name"],
                 sample=SAMPLES,
                 output_type=("sam.gz", "covstats.txt", "rpkm.txt"))
-        counts_table = expand(str(OUTDIR/"bbmap/{db_name}/counts.{column}.txt"),
+        counts_table = expand(str(OUTDIR/"bbmap/{db_name}/counts.{column}.tsv"),
                 db_name=bbmap_config["db_name"],
                 column=map(str.strip, bbmap_config["counts_table"]["columns"].split(",")))
         featureCounts = expand(str(OUTDIR/"bbmap/{db_name}/all_samples.featureCounts{output_type}"),
@@ -103,7 +103,7 @@ for bbmap_config in config["bbmap"]:
                     db_name=bbmap_config["db_name"],
                     sample=SAMPLES)
         output:
-            expand(str(OUTDIR/"bbmap/{db_name}/counts.{column}.txt"),
+            expand(str(OUTDIR/"bbmap/{db_name}/counts.{column}.tsv"),
                     db_name=bbmap_config["db_name"],
                     column=map(str.strip, bbmap_config["counts_table"]["columns"].split(","))
             )