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increase ref-based assembly mem #157

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merged 5 commits into from
Oct 1, 2020
Merged

increase ref-based assembly mem #157

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4ce4e80
increase mem of assemble_refbased
tomkinsc Sep 29, 2020
f0c513a
(re)parameterize memory for task align_reads
tomkinsc Sep 29, 2020
5c771d8
increase JVMmemory for task align_reads
tomkinsc Sep 30, 2020
28768d9
set --JVMmemory to 90% of instance mem in task align_reads
tomkinsc Sep 30, 2020
ac8568b
Merge branch 'master' into ct-increase-assembly-mem
dpark01 Oct 1, 2020
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7 changes: 5 additions & 2 deletions pipes/WDL/tasks/tasks_assembly.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -259,6 +259,7 @@ task align_reads {
String? aligner_options
Boolean? skip_mark_dupes=false

Int? machine_mem_gb
String docker="quay.io/broadinstitute/viral-core:2.1.8"

String sample_name = basename(basename(basename(reads_unmapped_bam, ".bam"), ".taxfilt"), ".clean")
Expand All @@ -273,6 +274,8 @@ task align_reads {

read_utils.py --version | tee VERSION

mem_in_mb=$(/opt/viral-ngs/source/docker/calc_mem.py mb 90)

cp ${reference_fasta} assembly.fasta
grep -v '^>' assembly.fasta | tr -d '\n' | wc -c | tee assembly_length

Expand All @@ -297,7 +300,7 @@ task align_reads {
--aligner ${aligner} \
${'--aligner_options "' + aligner_options + '"'} \
${true='--skipMarkDupes' false="" skip_mark_dupes} \
--JVMmemory=3g \
--JVMmemory "$mem_in_mb"m \
${"--NOVOALIGN_LICENSE_PATH=" + novocraft_license} \
--loglevel=DEBUG

Expand Down Expand Up @@ -350,7 +353,7 @@ task align_reads {

runtime {
docker: "${docker}"
memory: "7 GB"
memory: select_first([machine_mem_gb, 15]) + " GB"
cpu: 8
disks: "local-disk 375 LOCAL"
dx_instance_type: "mem1_ssd1_v2_x8"
Expand Down