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Updating Picard version in mitochondria WDL #5818

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Mar 21, 2019
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Merged

Updating Picard version in mitochondria WDL #5818

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4 changes: 2 additions & 2 deletions scripts/mitochondria_m2_wdl/AlignAndCall.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -273,7 +273,7 @@ task CollectWgsMetrics {
preemptible: select_first([preemptible_tries, 5])
memory: "3 GB"
disks: "local-disk " + disk_size + " HDD"
docker: "us.gcr.io/broad-gotc-prod/genomes-in-the-cloud:2.4.1-1540490856"
docker: "us.gcr.io/broad-gotc-prod/genomes-in-the-cloud:2.4.2-1552931386"
}
output {
File metrics = "metrics.txt"
Expand Down Expand Up @@ -325,7 +325,7 @@ task LiftoverAndCombineVcfs {
runtime {
disks: "local-disk " + disk_size + " HDD"
memory: "1200 MB"
docker: "us.gcr.io/broad-gotc-prod/genomes-in-the-cloud:2.4.1-1540490856"
docker: "us.gcr.io/broad-gotc-prod/genomes-in-the-cloud:2.4.2-1552931386"
preemptible: select_first([preemptible_tries, 5])
}
output{
Expand Down
6 changes: 3 additions & 3 deletions scripts/mitochondria_m2_wdl/AlignmentPipeline.wdl
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Expand Up @@ -143,7 +143,7 @@ task AlignAndMarkDuplicates {
memory: "6 GB"
cpu: "2"
disks: "local-disk " + disk_size + " HDD"
docker: "us.gcr.io/broad-gotc-prod/genomes-in-the-cloud:2.4.1-1540490856"
docker: "us.gcr.io/broad-gotc-prod/genomes-in-the-cloud:2.4.2-1552931386"
}
output {
File output_bam = "${output_bam_basename}.bam"
Expand All @@ -166,9 +166,9 @@ task GetBwaVersion {
}
runtime {
memory: "1 GB"
docker: "us.gcr.io/broad-gotc-prod/genomes-in-the-cloud:2.4.1-1540490856"
docker: "us.gcr.io/broad-gotc-prod/genomes-in-the-cloud:2.4.2-1552931386"
}
output {
String version = read_string(stdout())
}
}
}
6 changes: 3 additions & 3 deletions scripts/mitochondria_m2_wdl/MitochondriaPipeline.wdl
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Expand Up @@ -190,7 +190,7 @@ task SubsetBam {
runtime {
memory: "3 GB"
disks: "local-disk " + disk_size + " HDD"
docker: "us.gcr.io/broad-gotc-prod/genomes-in-the-cloud:2.4.1-1540490856"
docker: "us.gcr.io/broad-gotc-prod/genomes-in-the-cloud:2.4.2-1552931386"
preemptible: final_preemptible_tries
}
output {
Expand Down Expand Up @@ -262,7 +262,7 @@ task RevertSam {
runtime {
disks: "local-disk " + disk_size + " HDD"
memory: "2 GB"
docker: "us.gcr.io/broad-gotc-prod/genomes-in-the-cloud:2.4.1-1540490856"
docker: "us.gcr.io/broad-gotc-prod/genomes-in-the-cloud:2.4.2-1552931386"
preemptible: select_first([preemptible_tries, 5])
}
output {
Expand Down Expand Up @@ -339,7 +339,7 @@ task CoverageAtEveryBase {
runtime {
disks: "local-disk " + disk_size + " HDD"
memory: "1200 MB"
docker: "us.gcr.io/broad-gotc-prod/genomes-in-the-cloud:2.4.1-1540490856"
docker: "us.gcr.io/broad-gotc-prod/genomes-in-the-cloud:2.4.2-1552931386"
preemptible: select_first([preemptible_tries, 5])
}
output {
Expand Down