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Made runtime attrs to args in MT pipeline #8417

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merged 7 commits into from
Jul 14, 2023
Merged

Made runtime attrs to args in MT pipeline #8417

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2d47f0f
testing
dyeramosu Jul 12, 2023
9064bff
Merge pull request #1 from dyeramosu/test-alignment-wdl
dyeramosu Jul 12, 2023
1ab1c66
testing 2
dyeramosu Jul 12, 2023
82035d0
Merge pull request #2 from dyeramosu/test-alignment-wdl
dyeramosu Jul 12, 2023
98b94b9
testing
dyeramosu Jul 12, 2023
6bfdb91
Merge pull request #3 from dyeramosu/test-alignment-wdl
dyeramosu Jul 12, 2023
1ccbc69
Merge branch 'broadinstitute:master' into master
dyeramosu Jul 14, 2023
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10 changes: 7 additions & 3 deletions scripts/mitochondria_m2_wdl/AlignmentPipeline.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,8 @@ workflow AlignmentPipeline {

#Optional runtime arguments
Int? preemptible_tries
Int disk_size = ceil(size(input_bam, "GB") * 4 + size(mt_fasta, "GB") + size(mt_fasta_index, "GB") + size(mt_amb, "GB") + size(mt_ann, "GB") + size(mt_bwt, "GB") + size(mt_pac, "GB") + size(mt_sa, "GB")) + 20
Int mem = 6
}

parameter_meta {
Expand All @@ -43,7 +45,9 @@ workflow AlignmentPipeline {
ref_bwt = mt_bwt,
ref_pac = mt_pac,
ref_sa = mt_sa,
preemptible_tries = preemptible_tries
preemptible_tries = preemptible_tries,
disk_size = disk_size,
mem = mem
}

output {
Expand Down Expand Up @@ -72,8 +76,8 @@ task AlignAndMarkDuplicates {

# runtime
Int? preemptible_tries
Int disk_size = ceil(size(input_bam, "GB") * 4 + size(ref_fasta, "GB") + size(ref_fasta_index, "GB") + size(ref_amb, "GB") + size(ref_ann, "GB") + size(ref_bwt, "GB") + size(ref_pac, "GB") + size(ref_sa, "GB")) + 20
Int mem = 6
Int disk_size
Int mem
}

String basename = basename(input_bam, ".bam")
Expand Down