fix Star crash by removing the hard coded '--outSAMtype BAM SortedByC…

…oordinate' parameter from rule 'align'; this Star parameter is now solely defined in config.yaml
snakemake-workflows · Sep 6, 2021 · 5526842 · 5526842
1 parent 57f9f72
commit 5526842
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/workflow/rules/align.smk b/workflow/rules/align.smk
@@ -9,7 +9,7 @@ rule align:
         "logs/star/{sample}-{unit}.log",
     params:
         index=lambda wc, input: input.index,
-        extra="--outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --sjdbGTFfile {} {}".format(
+        extra="--quantMode GeneCounts --sjdbGTFfile {} {}".format(
             "resources/genome.gtf", config["params"]["star"]
         ),
     threads: 24