allow for gatk to be overridden, update with known good jar #7758
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RoriCremer
reviewed
Apr 6, 2022
| @@ -14,6 +14,8 @@ workflow GvsCreateFilterSet { | |||
| Array[String] snp_recalibration_annotation_values = ["AS_QD", "AS_MQRankSum", "AS_ReadPosRankSum", "AS_FS", "AS_MQ", "AS_SOR"] | |||
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| File interval_list = "gs://gcp-public-data--broad-references/hg38/v0/wgs_calling_regions.hg38.noCentromeres.noTelomeres.interval_list" | |||
| File gatk_override = "gs://broad-dsp-spec-ops/scratch/bigquery-jointcalling/jars/ah_var_store_20220406/gatk-package-4.2.0.0-480-gb62026a-SNAPSHOT-local.jar" | |||
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Is there a way to store this as a var in all the WDLs so we only have to update it in one place and wont accidentally miss workflows?
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and maybe do GvsPrepareRangesCallset too?
....and we should really delete the orig GvsPrepareCallset!
RoriCremer
approved these changes
Apr 6, 2022
This was referenced Mar 17, 2023
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