removing log directives

LiaOb21 · Jan 4, 2024 · dcad458 · dcad458
1 parent 7dd13e0
commit dcad458
Showing 1 changed file with 4 additions and 4 deletions.
diff --git a/workflow/rules/picard.smk b/workflow/rules/picard.smk
@@ -21,8 +21,8 @@ rule picard:
         """
         mkdir -p results/arima_mapping_pipeline/PAIR_DIR/
         mkdir -p results/arima_mapping_pipeline/REP_DIR/
-        java -Xmx4G -Djava.io.tmpdir=temp/ -jar {PICARD} AddOrReplaceReadGroups INPUT={input.tmp_bam} OUTPUT={output.bam_paired} ID={wildcards.sample} LB={wildcards.sample} SM={wildcards.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=results/arima_mapping_pipeline/TMP_DIR ASSUME_SORTED=TRUE VALIDATION_STRINGENCY=LENIENT REMOVE_DUPLICATES=TRUE >> {log} 2>&1
-        samtools index {output.mark_dup} >> {log} 2>&1
-        perl scripts/get_stats.pl {output.mark_dup} > {output.stats} >> {log} 2>&1
+        java -Xmx4G -Djava.io.tmpdir=temp/ -jar {PICARD} AddOrReplaceReadGroups INPUT={input.tmp_bam} OUTPUT={output.bam_paired} ID={wildcards.sample} LB={wildcards.sample} SM={wildcards.sample} PL=ILLUMINA PU=none 
+        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=results/arima_mapping_pipeline/TMP_DIR ASSUME_SORTED=TRUE VALIDATION_STRINGENCY=LENIENT REMOVE_DUPLICATES=TRUE
+        samtools index {output.mark_dup}
+        perl scripts/get_stats.pl {output.mark_dup} > {output.stats}
         """