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Commits on Feb 21, 2017

• Merge pull request #90 from tmooney/add_gt_expected_gzipped_input

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Commits on Feb 16, 2017

• Strelka2 gzips its outputs, so expect that in the subsequent step.

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Commits on Feb 14, 2017

• Merge pull request #82 from tmooney/add_travis_yml

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• Add setuptools dependency.

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• Run CWL validation with Travis CI.

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Commits on Feb 13, 2017

• Merge pull request #79 from tmooney/reconcile_more_bai_extensions

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• Whitespace.

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• Use "^.bai" consistently within Pindel workflow.

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Commits on Jan 25, 2017

• Merge pull request #68 from tmooney/few_more_secondary_files_as_arrays

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• Add a few more brackets around some secondaryFile extensions.

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Commits on Jan 24, 2017

• Merge pull request #65 from tmooney/revise_sambamba_resource_requests

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• Merge pull request #66 from tmooney/specify_secondary_files_as_array

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Commits on Jan 23, 2017

• Specify all secondary file suffixes as arrays.

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• Reduce sambamba memory to 12G; specify the resource request in CWL.

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Commits on Dec 21, 2016

• Convert pipeline to use Strelka2.

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• Merge pull request #53 from tmooney/somatic_pipeline

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Commits on Dec 19, 2016

• Merge pull request #52 from tmooney/add_roi_support

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• Implement name change from 1c90d18ef4d5c6bb06c5b2db45d997cfb1a3e9dc.

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• Move split_interval_list.cwl into generic detect_variants directory.

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• Merge branch 'master' into add_roi_support

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Commits on Dec 15, 2016

• Merge pull request #40 from tmooney/mutect_dbsnp_cosmic

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• Add ".alt" secondary file based on bd561bd9639b63480bb5bb508e42a76e4a500c20.

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• Combine two dbSNP inputs into one.

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• Switch to assuming a gzipped VCF with tabix index.

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• Overarching pipeline for somatic alignment + variant detection.

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• More readable Perl scripts :)

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Commits on Dec 14, 2016

• Post-filter Strelka VCF to limit to ROI.

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• New tool to limit variants to an ROI interval list.

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• Supply a BED file to limit Varscan detection to an ROI.

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• Integrate interval_list splitting into the mutect workflow.

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Commits on Dec 13, 2016

• A cwl command to convert an interval list to BED.

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• A CWL command to split an interval list.

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Commits on Dec 6, 2016

• Add support for dbSNP and COSMIC inputs to Mutect step.

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Commits on Oct 18, 2016

• Merge pull request #25 from tmooney/detect_variants

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Commits on Oct 11, 2016

• Give merged file a .gz filename.

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