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Cromwell-on-Azure #6

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Cromwell-on-Azure #6

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44ceb3a
For Cromwell-on-Azure compatibility, remove . in the output and chang…
byoo May 25, 2024
2c5ffbd
increase more disk space for hiphase_with_somatic
byoo May 25, 2024
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4 changes: 2 additions & 2 deletions hifisomatic.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -507,7 +507,7 @@ workflow hifisomatic {
input:
referenceName = patient + ".normal",
tumorName = patient + ".tumor",
outputDir = "./purple",
outputDir = "purple",
amberOutput = Amber.outputs,
cobaltOutput = Cobalt.outputs,
referenceFasta = ref_fasta,
Expand All @@ -522,7 +522,7 @@ workflow hifisomatic {
input:
referenceName = patient + ".normal",
tumorName = patient + ".tumor",
outputDir = "./purple",
outputDir = "purple",
amberOutput = Amber.outputs,
cobaltOutput = Cobalt.outputs,
somaticVcf = select_first([gather_ClairS.output_vcf]),
Expand Down
6 changes: 3 additions & 3 deletions tasks/alignment.wdl
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Expand Up @@ -29,7 +29,7 @@ task Align {
--sort -j ~{threads} \
--unmapped \
--preset HIFI \
--log-level INFO --log-file pbmm2.log
--log-level DEBUG --log-file pbmm2.log
>>>

output {
Expand All @@ -39,7 +39,7 @@ task Align {
}

runtime {
docker: "quay.io/biocontainers/pbmm2:1.12.0--h9ee0642_0"
docker: "quay.io/biocontainers/pbmm2:1.13.1--h9ee0642_0"
cpu: threads
memory: "~{threads * 4} GB"
disk: file_size + " GB"
Expand Down Expand Up @@ -116,4 +116,4 @@ task IndexBam {
maxRetries: 2
preemptible: 1
}
}
}
2 changes: 1 addition & 1 deletion tasks/annotation.wdl
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Expand Up @@ -151,4 +151,4 @@ task chord_hrd {
maxRetries: 2
preemptible: 1
}
}
}
6 changes: 3 additions & 3 deletions tasks/clonality.wdl
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Expand Up @@ -8,7 +8,7 @@ task Amber {
String tumorName
File tumorBam
File tumorBamIndex
String outputDir = "./amber"
String outputDir = "amber"
File ensembl_data_dir_tarball
File referenceFasta
File referenceFastaFai
Expand Down Expand Up @@ -76,7 +76,7 @@ task Cobalt {
File referenceFasta
File referenceFastaFai
File referenceFastaDict
String outputDir = "./cobalt"
String outputDir = "cobalt"
File ensembl_data_dir_tarball
Int threads
}
Expand Down Expand Up @@ -132,7 +132,7 @@ task Purple {
input {
String referenceName
String tumorName
String outputDir = "./purple"
String outputDir = "purple"
Array[File]+ amberOutput
Array[File]+ cobaltOutput
File? somaticVcf
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2 changes: 1 addition & 1 deletion tasks/deepsomatic.wdl
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Expand Up @@ -315,4 +315,4 @@ task correct_vcf {
maxRetries: 2
preemptible: 1
}
}
}
8 changes: 4 additions & 4 deletions tasks/phasing.wdl
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Expand Up @@ -45,7 +45,7 @@ task hiphase {
docker: "quay.io/pacbio/hiphase@sha256:c46c8493be8b308c0433441cbafcc1b6ac999dfa6e85001d466ebd551c4a8cf0"
cpu: threads
memory: "~{threads * 6} GB"
disk: file_size
disk: file_size + " GB"
maxRetries: 2
preemptible: 1
}
Expand All @@ -65,7 +65,7 @@ task hiphase_with_somatic {
Int threads
}

Float file_size = ceil(size(bam, "GB") + size(vcf, "GB") + size(ref_fasta, "GB") + 20)
Float file_size = ceil(size(bam, "GB") + size(vcf, "GB") + size(ref_fasta, "GB") + 100)

command <<<
set -euxo pipefail
Expand Down Expand Up @@ -101,7 +101,7 @@ task hiphase_with_somatic {
docker: "quay.io/pacbio/hiphase@sha256:c46c8493be8b308c0433441cbafcc1b6ac999dfa6e85001d466ebd551c4a8cf0"
cpu: threads
memory: "~{threads * 6} GB"
disk: file_size
disk: file_size + " GB"
maxRetries: 2
preemptible: 1
}
Expand Down Expand Up @@ -171,7 +171,7 @@ task longphase_with_somatic {
docker: "quay.io/pacbio/longphase@sha256:2d57c35da90fc74f56574c439e1a44f74c7f787f3812de3c402cf9206c9d4be3"
cpu: threads
memory: "~{threads * 6} GB"
disk: file_size
disk: file_size + " GB"
maxRetries: 2
preemptible: 1
}
Expand Down