Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

change runtime attrs to args #8413

Merged
merged 11 commits into from
Jul 11, 2023
Merged

change runtime attrs to args #8413

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
11 commits
Select commit Hold shift + click to select a range
e51b1cf
updated RevertSam disk_size attribute
dyeramosu Jul 11, 2023
7f42359
updated CoverageAtEveryBase disk_size attr
dyeramosu Jul 11, 2023
030f171
updated CollectWgsMetrics disk_size attr
dyeramosu Jul 11, 2023
4b604e5
updated M2 task runtime attrs
dyeramosu Jul 11, 2023
eaaa1f4
updated runtime attrs for AlignAndMarkDuplicates
dyeramosu Jul 11, 2023
fa7ebab
updated memory attributes
dyeramosu Jul 11, 2023
1a1d164
updated memory attributes
dyeramosu Jul 11, 2023
72b8cc4
updated runtime attributes
dyeramosu Jul 11, 2023
075a711
cleaned up
dyeramosu Jul 11, 2023
f64adbb
cleaned up
dyeramosu Jul 11, 2023
a8810f2
made requested changes
dyeramosu Jul 11, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
11 changes: 6 additions & 5 deletions scripts/mitochondria_m2_wdl/AlignAndCall.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -308,12 +308,13 @@ task CollectWgsMetrics {
Int? read_length
Int? coverage_cap

# runtime
Int? preemptible_tries
Int disk_size = ceil(size(input_bam, "GB") + size(ref_fasta, "GB") + size(ref_fasta_index, "GB")) + 20
Int mem = 3
}

Int read_length_for_optimization = select_first([read_length, 151])
Float ref_size = size(ref_fasta, "GB") + size(ref_fasta_index, "GB")
Int disk_size = ceil(size(input_bam, "GB") + ref_size) + 20

meta {
description: "Collect coverage metrics"
Expand Down Expand Up @@ -345,7 +346,7 @@ task CollectWgsMetrics {
>>>
runtime {
preemptible: select_first([preemptible_tries, 5])
memory: "3 GB"
memory: mem + " GB"
disks: "local-disk " + disk_size + " HDD"
docker: "us.gcr.io/broad-gotc-prod/genomes-in-the-cloud:2.4.2-1552931386"
}
Expand Down Expand Up @@ -426,16 +427,16 @@ task M2 {
Boolean? make_bamout
Boolean compress
File? gatk_override

# runtime
String? gatk_docker_override
Int? mem
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I think the mem, command_mem, and machine_mem arguments for this task were already hooked up correctly. Since mem was an optional input you could override the memory for this task and the java command appropriately the way it was set up before.

Int? preemptible_tries
Int disk_size = ceil(size(input_bam, "GB") + size(ref_fasta, "GB") + size(ref_fai, "GB")) + 20
}

String output_vcf = "raw" + if compress then ".vcf.gz" else ".vcf"
String output_vcf_index = output_vcf + if compress then ".tbi" else ".idx"
Float ref_size = size(ref_fasta, "GB") + size(ref_fai, "GB")
Int disk_size = ceil(size(input_bam, "GB") + ref_size) + 20

# Mem is in units of GB but our command and memory runtime values are in MB
Int machine_mem = if defined(mem) then mem * 1000 else 3500
Expand Down
7 changes: 4 additions & 3 deletions scripts/mitochondria_m2_wdl/AlignmentPipeline.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -70,13 +70,14 @@ task AlignAndMarkDuplicates {

String? read_name_regex

# 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
}

String basename = basename(input_bam, ".bam")
String metrics_filename = basename + ".metrics"
Float ref_size = 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")
Int disk_size = ceil(size(input_bam, "GB") * 4 + ref_size) + 20

meta {
description: "Aligns with BWA and MergeBamAlignment, then Marks Duplicates. Outputs a coordinate sorted bam."
Expand Down Expand Up @@ -149,7 +150,7 @@ task AlignAndMarkDuplicates {
>>>
runtime {
preemptible: select_first([preemptible_tries, 5])
memory: "6 GB"
memory: mem + " GB"
cpu: "2"
disks: "local-disk " + disk_size + " HDD"
docker: "us.gcr.io/broad-gotc-prod/genomes-in-the-cloud:2.4.2-1552931386"
Expand Down
10 changes: 6 additions & 4 deletions scripts/mitochondria_m2_wdl/MitochondriaPipeline.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -201,6 +201,7 @@ task SubsetBamToChrM {

# runtime
Int? preemptible_tries
Int mem = 3
}
Float ref_size = if defined(ref_fasta) then size(ref_fasta, "GB") + size(ref_fasta_index, "GB") + size(ref_dict, "GB") else 0
Int disk_size = ceil(size(input_bam, "GB") + ref_size) + 20
Expand Down Expand Up @@ -232,7 +233,7 @@ task SubsetBamToChrM {
-O ~{basename}.bam
>>>
runtime {
memory: "3 GB"
memory: mem + " GB"
disks: "local-disk " + disk_size + " HDD"
docker: select_first([gatk_docker_override, "us.gcr.io/broad-gatk/gatk:4.1.7.0"])
preemptible: select_first([preemptible_tries, 5])
Expand All @@ -247,12 +248,12 @@ task RevertSam {
input {
File input_bam
String basename = basename(input_bam, ".bam")
Int machine_mem = 2000

# runtime
Int? preemptible_tries
Int machine_mem = 2000
Int disk_size = ceil(size(input_bam, "GB") * 2.5) + 20
}
Int disk_size = ceil(size(input_bam, "GB") * 2.5) + 20
Int java_mem = machine_mem - 1000

meta {
Expand Down Expand Up @@ -300,9 +301,10 @@ task CoverageAtEveryBase {
File shifted_ref_fasta_index
File shifted_ref_dict

# runtime
Int? preemptible_tries
Int disk_size = ceil(size(input_bam_regular_ref, "GB") + size(input_bam_shifted_ref, "GB") + size(ref_fasta, "GB") * 2) + 20
}
Int disk_size = ceil(size(input_bam_regular_ref, "GB") + size(input_bam_shifted_ref, "GB") + size(ref_fasta, "GB") * 2) + 20

meta {
description: "Remove this hack once there's a GVCF solution."
Expand Down
Loading