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ConvertPairedFastQToUnmappedBamWf_170107.inputs.json WDLs for generic conversion/reversion use cases Jan 22, 2017
ConvertPairedFastQToUnmappedBamWf_170107.wdl WDLs for generic conversion/reversion use cases Jan 22, 2017
ExtractSamHeadersWf_170107.inputs.json WDLs for trivial BAM manipulations Jan 21, 2017
ExtractSamHeadersWf_170107.wdl WDLs for trivial BAM manipulations Jan 21, 2017
GenotypeGVCFsScatterWf_170204.inputs.json WDLs for segments of the germline short variant calling pipeline Mar 6, 2017
GenotypeGVCFsScatterWf_170204.wdl WDLs for segments of the germline short variant calling pipeline Mar 6, 2017
HaplotypeCallerGvcfScatterWf_170204.inputs.json WDLs for segments of the germline short variant calling pipeline Mar 6, 2017
HaplotypeCallerGvcfScatterWf_170204.wdl WDLs for segments of the germline short variant calling pipeline Mar 6, 2017
JointDiscoveryWf_170305.inputs.json WDLs for segments of the germline short variant calling pipeline Mar 6, 2017
JointDiscoveryWf_170305.wdl WDLs for segments of the germline short variant calling pipeline Mar 6, 2017
README.md Update README.md Apr 21, 2017
RevertBamToUnmappedRGBamsWf_170107.inputs.json WDLs for generic conversion/reversion use cases Jan 22, 2017
RevertBamToUnmappedRGBamsWf_170107.wdl WDLs for generic conversion/reversion use cases Jan 22, 2017
RevertRGBamsToPairedFastQsWf_170107.inputs.json WDLs for generic conversion/reversion use cases Jan 22, 2017
RevertRGBamsToPairedFastQsWf_170107.wdl WDLs for generic conversion/reversion use cases Jan 22, 2017
ValidateBamsWf_170107.inputs.json WDLs for trivial BAM manipulations Jan 21, 2017
ValidateBamsWf_170107.wdl WDLs for trivial BAM manipulations Jan 21, 2017
VariantRecalibrationWf_170305.inputs.json WDLs for segments of the germline short variant calling pipeline Mar 6, 2017
VariantRecalibrationWf_170305.wdl WDLs for segments of the germline short variant calling pipeline Mar 6, 2017
generic.options.json WDLs for trivial BAM manipulations Jan 21, 2017

README.md

Content overview

This directory contains WDL scripts developed at the Broad Institute and supported by the DSDE group (which develops GATK, Picard and Cromwell/WDL among other things). These scripts are NOT run in production at Broad; for production pipeline scripts, see the broad_pipelines directory.

When these scripts get updated, old versions are stored in the archive directory. Versions are distinguished with a datestamp (format: YYMMDD). Each WDL script is accompanied by a JSON file of example inputs bearing the same name, with the .inputs.json extension instead of .wdl. Unless otherwise specified, all WDL scripts can be run with the generic options file generic.options.json.

Important limitations

These scripts are provided "as-is", without any guarantees as to performance or results. It is the responsibility of the user to test these scripts fully before running them in production.

Many parameters and implementation decisions are optimized for our use of the Google Cloud Platform. In some cases (such as dynamic filename modifications and extension swapping using the sub() function) the scripts may need to be modified in order to be run successfully on a different platform.