diff --git a/workflow/rules/picard.smk b/workflow/rules/picard.smk index 57abcd6..4918861 100644 --- a/workflow/rules/picard.smk +++ b/workflow/rules/picard.smk @@ -18,7 +18,7 @@ rule picard: "../envs/arima_mapping_pipeline.yaml" shell: """ - PICARD="{CONDA_PREFIX}/share/picard-*/picard.jar" >> {log} 2>&1 + PICARD="{CONDA_PREFIX}/share/picard-*/picard.jar" java -Xmx4G -Djava.io.tmpdir=temp/ -jar $PICARD AddOrReplaceReadGroups INPUT={input.tmp_bam} OUTPUT={output.bam_paired} ID={sample} LB={sample} SM={sample} PL=ILLUMINA PU=none >> {log} 2>&1 java -Xmx30G -XX:-UseGCOverheadLimit -Djava.io.tmpdir=temp/ -jar $PICARD MarkDuplicates INPUT={output.bam_paired} OUTPUT={output.mark_dup} METRICS_FILE={output.metrics} TMP_DIR={input.TMP_DIR} ASSUME_SORTED=TRUE VALIDATION_STRINGENCY=LENIENT REMOVE_DUPLICATES=TRUE >> {log} 2>&1 samtools index {output.mark_dup} >> {log} 2>&1