From eb07e4755fea96bd2b74feef4c4b510af55fb654 Mon Sep 17 00:00:00 2001 From: ryan-moreno Date: Sat, 29 Apr 2023 09:10:26 -0500 Subject: [PATCH 1/3] Limit task memory to 80% --- modules/nf-core/picard/collectmultiplemetrics/main.nf | 2 +- modules/nf-core/picard/markduplicates/main.nf | 2 +- modules/nf-core/picard/mergesamfiles/main.nf | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/nf-core/picard/collectmultiplemetrics/main.nf b/modules/nf-core/picard/collectmultiplemetrics/main.nf index 73cdaf3a..43cb91cf 100644 --- a/modules/nf-core/picard/collectmultiplemetrics/main.nf +++ b/modules/nf-core/picard/collectmultiplemetrics/main.nf @@ -28,7 +28,7 @@ process PICARD_COLLECTMULTIPLEMETRICS { if (!task.memory) { log.info '[Picard CollectMultipleMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' } else { - avail_mem = task.memory.giga + avail_mem = (task.memory.giga*0.8).intValue() } """ picard \\ diff --git a/modules/nf-core/picard/markduplicates/main.nf b/modules/nf-core/picard/markduplicates/main.nf index 14800392..e1e31765 100644 --- a/modules/nf-core/picard/markduplicates/main.nf +++ b/modules/nf-core/picard/markduplicates/main.nf @@ -28,7 +28,7 @@ process PICARD_MARKDUPLICATES { if (!task.memory) { log.info '[Picard MarkDuplicates] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' } else { - avail_mem = task.memory.giga + avail_mem = (task.memory.giga*0.8).intValue() } """ picard \\ diff --git a/modules/nf-core/picard/mergesamfiles/main.nf b/modules/nf-core/picard/mergesamfiles/main.nf index 6afda3b3..63ed0cd5 100644 --- a/modules/nf-core/picard/mergesamfiles/main.nf +++ b/modules/nf-core/picard/mergesamfiles/main.nf @@ -25,7 +25,7 @@ process PICARD_MERGESAMFILES { if (!task.memory) { log.info '[Picard MergeSamFiles] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' } else { - avail_mem = task.memory.giga + avail_mem = (task.memory.giga*0.8).intValue() } if (bam_files.size() > 1) { """ From db14fd7efbc54b2946f1488d10d7f32af1907389 Mon Sep 17 00:00:00 2001 From: ryan-moreno Date: Mon, 1 May 2023 10:30:13 -0500 Subject: [PATCH 2/3] Reduce available memory for mark duplicates --- modules/nf-core/picard/mergesamfiles/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/picard/mergesamfiles/main.nf b/modules/nf-core/picard/mergesamfiles/main.nf index 63ed0cd5..0bd6c800 100644 --- a/modules/nf-core/picard/mergesamfiles/main.nf +++ b/modules/nf-core/picard/mergesamfiles/main.nf @@ -25,7 +25,7 @@ process PICARD_MERGESAMFILES { if (!task.memory) { log.info '[Picard MergeSamFiles] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' } else { - avail_mem = (task.memory.giga*0.8).intValue() + avail_mem = (task.memory.giga*0.6).intValue() } if (bam_files.size() > 1) { """ From ed379da3f810c40bbe5cb0ce19e72e84260cca09 Mon Sep 17 00:00:00 2001 From: ryan-moreno Date: Mon, 1 May 2023 11:10:07 -0500 Subject: [PATCH 3/3] Change reduction back to 80% --- modules/nf-core/picard/mergesamfiles/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/picard/mergesamfiles/main.nf b/modules/nf-core/picard/mergesamfiles/main.nf index 0bd6c800..63ed0cd5 100644 --- a/modules/nf-core/picard/mergesamfiles/main.nf +++ b/modules/nf-core/picard/mergesamfiles/main.nf @@ -25,7 +25,7 @@ process PICARD_MERGESAMFILES { if (!task.memory) { log.info '[Picard MergeSamFiles] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' } else { - avail_mem = (task.memory.giga*0.6).intValue() + avail_mem = (task.memory.giga*0.8).intValue() } if (bam_files.size() > 1) { """