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

Updating picard version in QC.wdl to avoid error with updated Platform Name (PL) in the SAM/BAM/CRAM file. #1257

Open
wants to merge 7 commits into
base: develop
Choose a base branch
from
Open

Updating picard version in QC.wdl to avoid error with updated Platform Name (PL) in the SAM/BAM/CRAM file. #1257

Changes from all commits
Commits
Show all changes
7 commits
Select commit Hold shift + click to select a range
9f137a7
Merge pull request #1198 from broadinstitute/staging
nikellepetrillo Feb 7, 2024
92a887e
Merge pull request #1200 from broadinstitute/develop
nikellepetrillo Feb 7, 2024
045b998
Merge pull request #1202 from broadinstitute/staging
nikellepetrillo Feb 8, 2024
664f959
Merge pull request #1208 from broadinstitute/develop
nikellepetrillo Feb 16, 2024
b8a32c7
Merge pull request #1209 from broadinstitute/staging
nikellepetrillo Feb 20, 2024
7f142a7
Updated picard version to 3.1.1
jiveshs98 Apr 1, 2024
127b41d
Merge branch 'develop' into warp_jivesh
jiveshs98 Apr 3, 2024
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
26 changes: 13 additions & 13 deletions tasks/broad/Qc.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -34,7 +34,7 @@ task CollectQualityYieldMetrics {
OUTPUT=~{metrics_filename}
}
runtime {
docker: "us.gcr.io/broad-gotc-prod/picard-cloud:2.26.10"
docker: "us.gcr.io/broad-gotc-prod/picard-cloud:3.1.1"
disks: "local-disk " + disk_size + " HDD"
memory: "3500 MiB"
preemptible: preemptible_tries
Expand Down Expand Up @@ -72,7 +72,7 @@ task CollectUnsortedReadgroupBamQualityMetrics {
touch ~{output_bam_prefix}.insert_size_histogram.pdf
}
runtime {
docker: "us.gcr.io/broad-gotc-prod/picard-cloud:2.26.10"
docker: "us.gcr.io/broad-gotc-prod/picard-cloud:3.1.1"
memory: "7000 MiB"
disks: "local-disk " + disk_size + " HDD"
preemptible: preemptible_tries
Expand Down Expand Up @@ -124,7 +124,7 @@ task CollectReadgroupBamQualityMetrics {
METRIC_ACCUMULATION_LEVEL=READ_GROUP
}
runtime {
docker: "us.gcr.io/broad-gotc-prod/picard-cloud:2.26.10"
docker: "us.gcr.io/broad-gotc-prod/picard-cloud:3.1.1"
memory: "7000 MiB"
disks: "local-disk " + disk_size + " HDD"
preemptible: preemptible_tries
Expand Down Expand Up @@ -178,7 +178,7 @@ task CollectAggregationMetrics {
METRIC_ACCUMULATION_LEVEL=LIBRARY
}
runtime {
docker: "us.gcr.io/broad-gotc-prod/picard-cloud:2.26.10"
docker: "us.gcr.io/broad-gotc-prod/picard-cloud:3.1.1"
memory: "7000 MiB"
disks: "local-disk " + disk_size + " HDD"
preemptible: preemptible_tries
Expand Down Expand Up @@ -229,7 +229,7 @@ task ConvertSequencingArtifactToOxoG {
--REFERENCE_SEQUENCE ~{ref_fasta}
}
runtime {
docker: "us.gcr.io/broad-gotc-prod/picard-cloud:2.26.10"
docker: "us.gcr.io/broad-gotc-prod/picard-cloud:3.1.1"
memory: "~{memory_size} MiB"
disks: "local-disk " + disk_size + " HDD"
preemptible: preemptible_tries
Expand Down Expand Up @@ -267,7 +267,7 @@ task CrossCheckFingerprints {
CROSSCHECK_BY=~{cross_check_by}
>>>
runtime {
docker: "us.gcr.io/broad-gotc-prod/picard-cloud:2.26.10"
docker: "us.gcr.io/broad-gotc-prod/picard-cloud:3.1.1"
preemptible: preemptible_tries
memory: "3500 MiB"
disks: "local-disk " + disk_size + " HDD"
Expand Down Expand Up @@ -337,7 +337,7 @@ task CheckFingerprintTask {
>>>

runtime {
docker: "us.gcr.io/broad-gotc-prod/picard-cloud:2.26.10"
docker: "us.gcr.io/broad-gotc-prod/picard-cloud:3.1.1"
disks: "local-disk " + disk_size + " HDD"
memory: "~{memory_size} MiB"
preemptible: preemptible_tries
Expand Down Expand Up @@ -437,7 +437,7 @@ task ValidateSamFile {
IS_BISULFITE_SEQUENCED=false
}
runtime {
docker: "us.gcr.io/broad-gotc-prod/picard-cloud:2.26.10"
docker: "us.gcr.io/broad-gotc-prod/picard-cloud:3.1.1"
preemptible: preemptible_tries
memory: "~{memory_size} MiB"
disks: "local-disk " + disk_size + " HDD"
Expand Down Expand Up @@ -475,7 +475,7 @@ task CollectWgsMetrics {
READ_LENGTH=~{read_length}
}
runtime {
docker: "us.gcr.io/broad-gotc-prod/picard-cloud:2.26.10"
docker: "us.gcr.io/broad-gotc-prod/picard-cloud:3.1.1"
preemptible: preemptible_tries
memory: "3000 MiB"
disks: "local-disk " + disk_size + " HDD"
Expand Down Expand Up @@ -518,7 +518,7 @@ task CollectRawWgsMetrics {
READ_LENGTH=~{read_length}
}
runtime {
docker: "us.gcr.io/broad-gotc-prod/picard-cloud:2.26.10"
docker: "us.gcr.io/broad-gotc-prod/picard-cloud:3.1.1"
preemptible: preemptible_tries
memory: "~{memory_size} GiB"
disks: "local-disk " + disk_size + " HDD"
Expand Down Expand Up @@ -567,7 +567,7 @@ task CollectHsMetrics {
}

runtime {
docker: "us.gcr.io/broad-gotc-prod/picard-cloud:2.26.10"
docker: "us.gcr.io/broad-gotc-prod/picard-cloud:3.1.1"
preemptible: preemptible_tries
memory: "~{memory_size} MiB"
disks: "local-disk " + disk_size + " HDD"
Expand Down Expand Up @@ -596,7 +596,7 @@ task CalculateReadGroupChecksum {
OUTPUT=~{read_group_md5_filename}
}
runtime {
docker: "us.gcr.io/broad-gotc-prod/picard-cloud:2.26.10"
docker: "us.gcr.io/broad-gotc-prod/picard-cloud:3.1.1"
preemptible: preemptible_tries
memory: "4000 MiB"
disks: "local-disk " + disk_size + " HDD"
Expand Down Expand Up @@ -689,7 +689,7 @@ task CollectVariantCallingMetrics {
~{true="GVCF_INPUT=true" false="" is_gvcf}
}
runtime {
docker: "us.gcr.io/broad-gotc-prod/picard-cloud:2.26.10"
docker: "us.gcr.io/broad-gotc-prod/picard-cloud:3.1.1"
preemptible: preemptible_tries
memory: "3000 MiB"
disks: "local-disk " + disk_size + " HDD"
Expand Down