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Pre-emptible instances #13

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Pre-emptible instances #13

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37 changes: 6 additions & 31 deletions wdl/align_trimmed/align_trimmed.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -9,11 +9,12 @@ task alignTrimmed {
String SID
Int bismark_multicore
# Multiply by ~4 to get number of cores required
#If you increase the multicore to 6 make sure to double up the memory to 80, otherwise you will loose 20-30% of the reads
#If you increase the multicore to 6 make sure to double up the memory to 80, otherwise you will lose 20-30% of the reads
Int ncpu
Int memory
Int disk
Int ncpu
String docker
Int preemptible = 0
}

String genome_dir = basename(genome_dir_tar, ".tar.gz")
Expand Down Expand Up @@ -81,40 +82,14 @@ task alignTrimmed {
}

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

meta {
author: "Samir Akre"
}
}

workflow align_trimmed {
input {
Int memory
Int disk
Int ncpu
String docker

String SID
}

call alignTrimmed {
input:
memory=memory,
disk=disk,
ncpu=ncpu,
docker=docker,
SID=SID
}

output {
File bismark_align_log = alignTrimmed.bismark_align_log
File bismark_report = alignTrimmed.bismark_report
File bismark_reads = alignTrimmed.bismark_reads
}
}

10 changes: 4 additions & 6 deletions wdl/bowtie2_align/bowtie2_align.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,7 @@ task bowtie2_align {
Int disk
Int ncpu
String docker
Int preemptible = 2
}

String genome_dir = basename(genome_dir_tar, ".tar.gz")
Expand Down Expand Up @@ -59,17 +60,14 @@ task bowtie2_align {
}

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

meta {
author: "Archana Raja"
}
}

workflow bowtie2_align_workflow {
call bowtie2_align
}
21 changes: 4 additions & 17 deletions wdl/collect_qc_metrics/collect_qc_metrics.wdl
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Expand Up @@ -17,6 +17,7 @@ task collectQCMetrics {
Int disk
Int ncpu
String docker
Int preemptible = 2
}

parameter_meta {
Expand Down Expand Up @@ -72,28 +73,14 @@ task collectQCMetrics {
}

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

meta {
author: "Samir Akre,Archana Raja"
}
}

workflow collect_qc_metrics {
input {
Int memory
Int disk
Int ncpu
}

call collectQCMetrics {
input:
memory=memory,
disk=disk,
ncpu=ncpu
}
}
6 changes: 4 additions & 2 deletions wdl/compute_mapped/chr_info.wdl
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Expand Up @@ -10,6 +10,7 @@ task samtools_mapped {
Int disk
Int ncpu
String docker
Int preemptible = 2
}

parameter_meta {
Expand Down Expand Up @@ -39,10 +40,11 @@ task samtools_mapped {
}

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

meta {
Expand Down
28 changes: 5 additions & 23 deletions wdl/index_genomes/Bismark_IndexGenomes.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@ task indexGenome {
Int disk
Int ncpu
String docker
Int preemptible = 2
}

# Makes genome directory with input files for use with bismark
Expand Down Expand Up @@ -56,34 +57,15 @@ task indexGenome {
}

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

meta {
author: "Samir Akre"
}

}

workflow Bismark_Index_Generation {
input {
Int memory
Int disk
Int ncpu
String docker
}

call indexGenome {
input:
memory=memory,
disk=disk,
ncpu=ncpu,
docker=docker
}

output {
File bsGenome = indexGenome.bsGenome
}
}
23 changes: 4 additions & 19 deletions wdl/mark_duplicates/mark_duplicates.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@ task markDuplicates {
Int disk
Int ncpu
String docker
Int preemptible = 2
}

parameter_meta {
Expand Down Expand Up @@ -37,30 +38,14 @@ task markDuplicates {
}

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

meta {
author: "Samir Akre"
}
}

workflow mark_duplicates {
input {
Int memory
Int disk
Int ncpu
String docker
}

call markDuplicates {
input:
memory=memory,
disk=disk,
ncpu=ncpu,
docker=docker
}
}
23 changes: 4 additions & 19 deletions wdl/mark_umi_dup/mark_udup.wdl
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Expand Up @@ -9,6 +9,7 @@ task tag_udup {
Int disk
Int ncpu
String docker
Int preemptible = 2
}

parameter_meta {
Expand All @@ -35,30 +36,14 @@ task tag_udup {
}

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

meta {
author: "Samir Akre"
}
}

workflow mark_udup {
input {
Int memory
Int disk
Int ncpu
String docker
}

call tag_udup {
input:
memory=memory,
disk=disk,
ncpu=ncpu,
docker=docker
}
}
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 @@ -9,6 +9,7 @@ task merge_results {
Int disk
Int ncpu
String docker
Int preemptible = 2
}

parameter_meta {
Expand Down Expand Up @@ -39,9 +40,10 @@ task merge_results {
}

runtime {
docker: "${docker}"
cpu: ncpu
docker: docker
memory: "${memory}GB"
disks: "local-disk ${disk} HDD"
cpu: "${ncpu}"
preemptible: preemptible
}
}
40 changes: 6 additions & 34 deletions wdl/quantify_methylation/quantify_methylation.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,7 @@ task quantifyMethylation {
Int disk
Int ncpu
String docker
Int preemptible = 2
}

parameter_meta {
Expand Down Expand Up @@ -68,46 +69,17 @@ task quantifyMethylation {
File bismark_summary_report = "bismark_summary_report.txt"
File bismark_summary_html = "bismark_summary_report.html"
File bismark_report_html = "${SID}.html"

}

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

meta {
author: "Samir Akre"
}
}

workflow quantify_methylation {
input {
String SID
Int memory
Int disk
Int ncpu
String docker
}

call quantifyMethylation {
input:
memory=memory,
disk=disk,
ncpu=ncpu,
docker=docker,
SID=SID
}
output {
File CpG_context=quantifyMethylation.CpG_context
File CHG_context=quantifyMethylation.CHG_context
File CHH_context=quantifyMethylation.CHH_context
File M_Bias=quantifyMethylation.M_Bias
File bedgraph=quantifyMethylation.bedgraph
File bismark_cov=quantifyMethylation.bismark_cov
File splitting_report=quantifyMethylation.splitting_report
File bismark_summary_report =quantifyMethylation.bismark_summary_report
File bismark_summary_html =quantifyMethylation.bismark_summary_html
File bismark_report_html =quantifyMethylation.bismark_report_html
}
}
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