fix: picard has a different CLI when installed via conda

CCBR · Apr 30, 2024 · 45d981a · 45d981a
1 parent b3ebb45
commit 45d981a
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/workflow/rules/align.smk b/workflow/rules/align.smk
@@ -654,6 +654,6 @@ rule estimate_duplication:
     shell:
         """
 set -exo pipefail
-java -Xmx{params.memG} -jar ${{PICARD_JARPATH}}/picard.jar MarkDuplicates I={input.bam} O=/dev/shm/{params.sample}.mark_dup.bam M={output.metrics}
+picard -Xmx{params.memG} MarkDuplicates -I={input.bam} -O=/dev/shm/{params.sample}.mark_dup.bam -M={output.metrics}
 rm -f /dev/shm/{params.sample}*
 """