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Pre-emptible VMs and other fixes #65

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Pre-emptible VMs and other fixes #65

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482e03d
feat: add pre-emptible runtime attribute to each task [closes MoTrPAC…
mihirsamdarshi Aug 7, 2024
52248e0
fix: change name of input variable to align with other MoTrPAC pipelines
mihirsamdarshi Aug 9, 2024
595e4c4
fix: align cutadapt CPU runtime parameter naming with other tasks
mihirsamdarshi Aug 9, 2024
1c7f4de
fix: add preemptible attribute to mark duplicates
mihirsamdarshi Oct 10, 2024
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7 changes: 4 additions & 3 deletions wdl/attach_umi/attach_umi.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,7 @@ task attachUMI {
Int memory
Int disk_space
Int ncpu
Int preemptible

String docker
}
Expand All @@ -34,11 +35,11 @@ task attachUMI {
}

runtime {
docker: "${docker}"
docker: docker
memory: "${memory}GB"
disks: "local-disk ${disk_space} HDD"
cpu: "${ncpu}"

cpu: ncpu
preemptible: preemptible
}

parameter_meta {
Expand Down
6 changes: 4 additions & 2 deletions wdl/bowtie2_align/bowtie2_align.wdl
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Expand Up @@ -11,6 +11,7 @@ task bowtie2_align {
Int memory
Int disk_space
Int ncpu
Int preemptible

String docker
}
Expand Down Expand Up @@ -43,10 +44,11 @@ task bowtie2_align {
}

runtime {
docker: "${docker}"
cpu: ncpu
memory: "${memory}GB"
disks: "local-disk ${disk_space} HDD"
cpu: "${ncpu}"
docker: docker
preemptible: preemptible
}

parameter_meta {
Expand Down
1 change: 1 addition & 0 deletions wdl/bowtie2_index/bowtie2_index.wdl
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Expand Up @@ -7,6 +7,7 @@ task bowtie2_index {
Int memory
Int disk_space
Int ncpu
Int preemptible

}

Expand Down
7 changes: 4 additions & 3 deletions wdl/checksum/compute_md5sum.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,7 @@ task checksum {
Int memory
Int disk_space
Int ncpu
Int preemptible

String docker
File fastq
Expand Down Expand Up @@ -57,7 +58,7 @@ task gather_checksums {
Int memory = 8
Int disk_space = 8
Int ncpu = 1
= 0
Int preemptible = 0
}

command <<<
Expand All @@ -76,7 +77,7 @@ task gather_checksums {
docker: "gcr.io/motrpac-portal/motrpac_rnaseq:v0.1_04_20_19"
memory: "${memory}GB"
disks: "local-disk ${disk_space} HDD"
cpu: "${ncpu}"

cpu: ncpu
preemptible: preemptible
}
}
9 changes: 4 additions & 5 deletions wdl/collect_qc_metrics/collect_qc.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ task rnaseqQC {
Int memory
Int disk_space
Int ncpu

Int preemptible
String docker

File trim_summary
Expand Down Expand Up @@ -51,11 +51,11 @@ task rnaseqQC {
}

runtime {
docker: "${docker}"
cpu: ncpu
memory: "${memory}GB"
disks: "local-disk ${disk_space} HDD"
cpu: "${ncpu}"

docker: docker
preemptible: preemptible
}

parameter_meta {
Expand Down Expand Up @@ -83,6 +83,5 @@ task rnaseqQC {
star_log: {
label: "STAR Align Log"
}

}
}
7 changes: 4 additions & 3 deletions wdl/collect_rnaseq_metrics/collect_rnaseq_metrics.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ task collectrnaseqmetrics {
Int memory
Int disk_space
Int ncpu

Int preemptible
String docker
}

Expand Down Expand Up @@ -41,10 +41,11 @@ task collectrnaseqmetrics {
}

runtime {
docker: "${docker}"
cpu: ncpu
memory: "${memory}GB"
disks: "local-disk ${disk_space} HDD"
cpu: "${ncpu}"
docker: docker
preemptible: preemptible
}

parameter_meta {
Expand Down
7 changes: 4 additions & 3 deletions wdl/compute_mapped/mapped.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ task samtools_mapped {
Int memory
Int disk_space
Int ncpu

Int preemptible
String docker
}

Expand Down Expand Up @@ -48,10 +48,11 @@ task samtools_mapped {
}

runtime {
docker: "${docker}"
cpu: ncpu
memory: "${memory}GB"
disks: "local-disk ${disk_space} HDD"
cpu: "${ncpu}"
docker: docker
preemptible: preemptible
}

parameter_meta {
Expand Down
9 changes: 5 additions & 4 deletions wdl/cutadapt/cutadapt.wdl
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Expand Up @@ -10,10 +10,10 @@ task Cutadapt {
String univ_adapter
Int? minimumLength

Int cpus
Int ncpu
Int disk_space
Int memory

Int preemptible
String docker
}

Expand Down Expand Up @@ -64,9 +64,10 @@ task Cutadapt {
}

runtime {
docker: "${docker}"
cpu: ncpu
memory: "${memory}GB"
disks: "local-disk ${disk_space} HDD"
cpu: "${cpus}"
docker: docker
preemptible: preemptible
}
}
7 changes: 4 additions & 3 deletions wdl/fastqc/fastqc.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@ task fastQC {
Int memory
Int disk_space
Int ncpu

Int preemptible
String docker
}

Expand Down Expand Up @@ -42,9 +42,10 @@ task fastQC {
}

runtime {
docker: "${docker}"
cpu: ncpu
memory: "${memory}GB"
disks: "local-disk ${disk_space} HDD"
cpu: "${ncpu}"
docker: docker
preemptible: preemptible
}
}
3 changes: 2 additions & 1 deletion wdl/feature_counts/fc.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ task feature_counts {
Int memory
Int disk_space
Int ncpu

Int preemptible
String docker
}

Expand All @@ -36,6 +36,7 @@ task feature_counts {
memory: "${memory}GB"
disks: "local-disk ${disk_space} HDD"
cpu: "${ncpu}"
preemptible: preemptible
}

parameter_meta {
Expand Down
8 changes: 4 additions & 4 deletions wdl/mark_duplicates/mark_duplicates.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@ task markduplicates {
Int memory
Int disk_space
Int ncpu

Int preemptible
String docker
}

Expand Down Expand Up @@ -44,11 +44,11 @@ task markduplicates {
}

runtime {
docker: "${docker}"
cpu: ncpu
memory: "${memory}GB"
disks: "local-disk ${disk_space} HDD"
cpu: "${ncpu}"

docker: docker
preemptible: preemptible
}

parameter_meta {
Expand Down
6 changes: 4 additions & 2 deletions wdl/merge_results/merge_results.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@ task merge_results {
Int memory
Int disk_space
Int ncpu
Int preemptible
String docker
}

Expand Down Expand Up @@ -58,9 +59,10 @@ task merge_results {
}

runtime {
docker: "${docker}"
cpu: ncpu
memory: "${memory}GB"
disks: "local-disk ${disk_space} HDD"
cpu: "${ncpu}"
docker: docker
preemptible: preemptible
}
}
8 changes: 4 additions & 4 deletions wdl/multiqc/multiqc.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ task multiQC {
Int memory
Int disk_space
Int ncpu

Int preemptible
String docker
}

Expand Down Expand Up @@ -47,11 +47,11 @@ task multiQC {
}

runtime {
docker: "${docker}"
cpu: ncpu
memory: "${memory}GB"
disks: "local-disk ${disk_space} HDD"
cpu: "${ncpu}"

docker: docker
preemptible: preemptible
}

parameter_meta {
Expand Down
7 changes: 4 additions & 3 deletions wdl/multiqc/multiqc_postalign.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@ task multiQC_postalign {
Int memory
Int disk_space
Int ncpu

Int preemptible
String docker
}

Expand Down Expand Up @@ -61,10 +61,11 @@ task multiQC_postalign {
}

runtime {
docker: "${docker}"
cpu: ncpu
memory: "${memory}GB"
disks: "local-disk ${disk_space} HDD"
cpu: "${ncpu}"
docker: docker
preemptible: preemptible
}

parameter_meta {
Expand Down
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