From bcb29a0662dfa5ea5abd3ef1b35dacb7634a720f Mon Sep 17 00:00:00 2001 From: David Brown Date: Mon, 25 Jul 2022 21:32:17 -0400 Subject: [PATCH] Update bwa_split.mk --- split_workflows/bwa_split.mk | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/split_workflows/bwa_split.mk b/split_workflows/bwa_split.mk index eb2241e0..49314213 100644 --- a/split_workflows/bwa_split.mk +++ b/split_workflows/bwa_split.mk @@ -211,20 +211,20 @@ $(foreach sample,$(SAMPLES),\ define picard-metrics metrics/$1.idx_stats.txt : bam/$1.bam - $$(call RUN, -c -n 1 -s 12G -m 24G,"set -o pipefail && \ + $$(call RUN, -c -n 1 -s 12G -m 24G -w 24:00:00,"set -o pipefail && \ $$(BAM_INDEX) \ INPUT=$$(<) \ > $$(@)") metrics/$1.aln_metrics.txt : bam/$1.bam - $$(call RUN, -c -n 1 -s 12G -m 24G,"set -o pipefail && \ + $$(call RUN, -c -n 1 -s 12G -m 24G -w 24:00:00,"set -o pipefail && \ $$(COLLECT_ALIGNMENT_METRICS) \ REFERENCE_SEQUENCE=$$(REF_FASTA) \ INPUT=$$(<) \ OUTPUT=$$(@)") metrics/$1.insert_metrics.txt : bam/$1.bam - $$(call RUN, -c -n 1 -s 12G -m 24G,"set -o pipefail && \ + $$(call RUN, -c -n 1 -s 12G -m 24G -w 24:00:00,"set -o pipefail && \ $$(COLLECT_INSERT_METRICS) \ INPUT=$$(<) \ OUTPUT=$$(@) \ @@ -232,14 +232,14 @@ metrics/$1.insert_metrics.txt : bam/$1.bam MINIMUM_PCT=0.5") metrics/$1.oxog_metrics.txt : bam/$1.bam - $$(call RUN, -c -n 1 -s 12G -m 24G,"set -o pipefail && \ + $$(call RUN, -c -n 1 -s 12G -m 24G -w 24:00:00,"set -o pipefail && \ $$(COLLECT_OXOG_METRICS) \ REFERENCE_SEQUENCE=$$(REF_FASTA) \ INPUT=$$(<) \ OUTPUT=$$(@)") metrics/$1.gc_metrics_summary.txt : bam/$1.bam - $$(call RUN, -c -n 1 -s 12G -m 24G,"set -o pipefail && \ + $$(call RUN, -c -n 1 -s 12G -m 24G -w 24:00:00,"set -o pipefail && \ $$(COLLECT_GC_BIAS) \ INPUT=$$(<) \ OUTPUT=metrics/$1.gc_metrics.txt \ @@ -248,7 +248,7 @@ metrics/$1.gc_metrics_summary.txt : bam/$1.bam SUMMARY_OUTPUT=$$(@)") metrics/$1.wgs_metrics.txt : bam/$1.bam - $$(call RUN, -c -n 1 -s 12G -m 24G,"set -o pipefail && \ + $$(call RUN, -c -n 1 -s 12G -m 24G -w 24:00:00,"set -o pipefail && \ $$(COLLECT_WGS_METRICS) \ INPUT=$$(<) \ OUTPUT=$$(@) \