Commit aebad7df authored by van den Berg's avatar van den Berg
Browse files

Add memory settings for hs_metrics and multiple_metrics

parent e2c4274e
...@@ -464,7 +464,7 @@ rule multiple_metrics: ...@@ -464,7 +464,7 @@ rule multiple_metrics:
alignment = "{sample}/bams/{sample}.alignment_summary_metrics", alignment = "{sample}/bams/{sample}.alignment_summary_metrics",
insertMetrics = "{sample}/bams/{sample}.insert_size_metrics" insertMetrics = "{sample}/bams/{sample}.insert_size_metrics"
container: containers["picard"] container: containers["picard"]
shell: "picard CollectMultipleMetrics " shell: "picard -Xmx8G -XX:CompressedClassSpaceSize=256m CollectMultipleMetrics "
"I={input.bam} O={params.prefix} " "I={input.bam} O={params.prefix} "
"R={input.ref} " "R={input.ref} "
"PROGRAM=CollectAlignmentSummaryMetrics " "PROGRAM=CollectAlignmentSummaryMetrics "
...@@ -501,7 +501,7 @@ rule hs_metrics: ...@@ -501,7 +501,7 @@ rule hs_metrics:
baits = rules.bed_to_interval.output.baits_interval, baits = rules.bed_to_interval.output.baits_interval,
output: "{sample}/bams/{sample}.hs_metrics.txt" output: "{sample}/bams/{sample}.hs_metrics.txt"
container: containers["picard"] container: containers["picard"]
shell: "picard CollectHsMetrics " shell: "picard -Xmx8G -XX:CompressedClassSpaceSize=256m CollectHsMetrics "
"I={input.bam} O={output} " "I={input.bam} O={output} "
"R={input.ref} " "R={input.ref} "
"BAIT_INTERVALS={input.baits} " "BAIT_INTERVALS={input.baits} "
......
...@@ -9,8 +9,14 @@ align: ...@@ -9,8 +9,14 @@ align:
bed_to_interval: bed_to_interval:
threads: 1 threads: 1
vmem: 16G vmem: 16G
hs_metrics:
threads: 1
vmem: 20G
markdup: markdup:
vmem: 20G vmem: 20G
multiple_metrics:
threads: 1
vmem: 20G
baserecal: baserecal:
threads: 8 threads: 8
vmem: 6G vmem: 6G
......
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