From 2d47f0fae5975dfc786fd824248469c830965d4b Mon Sep 17 00:00:00 2001 From: Deepika Yeramosu Date: Wed, 12 Jul 2023 10:11:24 -0400 Subject: [PATCH 1/3] testing --- scripts/mitochondria_m2_wdl/AlignmentPipeline.wdl | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/scripts/mitochondria_m2_wdl/AlignmentPipeline.wdl b/scripts/mitochondria_m2_wdl/AlignmentPipeline.wdl index 4c0dcc8c19c..153ac82faf9 100644 --- a/scripts/mitochondria_m2_wdl/AlignmentPipeline.wdl +++ b/scripts/mitochondria_m2_wdl/AlignmentPipeline.wdl @@ -21,6 +21,8 @@ workflow AlignmentPipeline { #Optional runtime arguments Int? preemptible_tries + Int disk_size + Int mem } parameter_meta { @@ -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 { From 1ab1c66598aa32055752327fb9afc14652bc86be Mon Sep 17 00:00:00 2001 From: Deepika Yeramosu Date: Wed, 12 Jul 2023 10:16:05 -0400 Subject: [PATCH 2/3] testing 2 --- scripts/mitochondria_m2_wdl/AlignmentPipeline.wdl | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/scripts/mitochondria_m2_wdl/AlignmentPipeline.wdl b/scripts/mitochondria_m2_wdl/AlignmentPipeline.wdl index 153ac82faf9..3b9ce303f62 100644 --- a/scripts/mitochondria_m2_wdl/AlignmentPipeline.wdl +++ b/scripts/mitochondria_m2_wdl/AlignmentPipeline.wdl @@ -21,8 +21,6 @@ workflow AlignmentPipeline { #Optional runtime arguments Int? preemptible_tries - Int disk_size - Int mem } parameter_meta { @@ -46,8 +44,8 @@ workflow AlignmentPipeline { ref_pac = mt_pac, ref_sa = mt_sa, preemptible_tries = preemptible_tries, - disk_size = disk_size, - mem = mem + 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, + mem = 6 } output { @@ -76,8 +74,8 @@ 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") From 98b94b974c3503da833e7521b0991cc973dc544f Mon Sep 17 00:00:00 2001 From: Deepika Yeramosu Date: Wed, 12 Jul 2023 10:27:13 -0400 Subject: [PATCH 3/3] testing --- scripts/mitochondria_m2_wdl/AlignmentPipeline.wdl | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/scripts/mitochondria_m2_wdl/AlignmentPipeline.wdl b/scripts/mitochondria_m2_wdl/AlignmentPipeline.wdl index 3b9ce303f62..64bf40f3c3f 100644 --- a/scripts/mitochondria_m2_wdl/AlignmentPipeline.wdl +++ b/scripts/mitochondria_m2_wdl/AlignmentPipeline.wdl @@ -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 { @@ -44,8 +46,8 @@ workflow AlignmentPipeline { ref_pac = mt_pac, ref_sa = mt_sa, preemptible_tries = preemptible_tries, - 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, - mem = 6 + disk_size = disk_size, + mem = mem } output { @@ -74,8 +76,8 @@ task AlignAndMarkDuplicates { # runtime Int? preemptible_tries - Int? disk_size - Int? mem + Int disk_size + Int mem } String basename = basename(input_bam, ".bam")