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Commits on Jul 2, 2018

• RNA-seq: provide general workflow fixes for variant calling

  chapmanb

  committed
  7ea627c

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Commits on Jun 30, 2018

• Test fixes: add UMI fastqs, avoid relative paths for Docker Cromwell tests

  chapmanb

  committed
  68c413b

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Commits on Jun 29, 2018

• somatic: modernize workflow in prep for testing germline calling support

  chapmanb

  committed
  7f62469

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• SV: add testing for tools_on and validation

  chapmanb

  committed
  073115f

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Commits on Jun 23, 2018

• RNA-seq: add Cromwell support for local runs

  chapmanb

  committed
  968b247

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Commits on Jun 18, 2018

• Fix cromwell execution (Docker) for CI tests; match latest CWL changes

  chapmanb

  committed
  a53d593

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Commits on Jun 12, 2018

• Joint workflow with Cromwell runner

  chapmanb

  committed
  5195fa7

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• QC only workflow with latest build and Toil/Cromwell runners

  chapmanb

  committed
  0ee5b53

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Commits on May 7, 2018

• Fix missing relative path to pre-created VCF inputs

  chapmanb

  committed
  54fbb49

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Commits on Apr 25, 2018

• Scripts for running Cromwell locally

  chapmanb

  committed
  25684c6

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• Example scripts for running Cromwell CWL on SLURM

  chapmanb

  committed
  aef8d9a

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Commits on Feb 28, 2018

• Test case for prealigned BAMs and precalled VCFs

  chapmanb

  committed
  988afb0

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Commits on Jan 13, 2018

• Ignore additional batch steps that do not need input files staged

  chapmanb

  committed
  aaa95b3

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Commits on Jan 12, 2018

• Allow null outputs for batch_samples

  chapmanb

  committed
  be4fdb9

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• DNAnexus test workflow with no to_rec staging

  chapmanb

  committed
  d6a6189

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• Merge pull request #3 from geetduggal/master

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  chapmanb

  authored
  d68a16e

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• Update to skip unnecessary downloads

  geetduggal

  committed
  bdfdd8d

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Commits on Jan 1, 2018

• Test data and inputs for RNA-seq workflow

  chapmanb

  committed
  5213f52

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Commits on Dec 31, 2017

• Test workflow for RNA-seq pipeline

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  chapmanb

  committed
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Commits on Dec 26, 2017

• Use container for travis CI toil test

  chapmanb

  committed
  84b551a

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• Cleanup: add missing fastqs, use containers for unit tests

  chapmanb

  committed
  8a2773f

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Commits on Dec 25, 2017

• Update arvados test CWL

  chapmanb

  committed
  d10f9d9

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Commits on Dec 20, 2017

• DNAnexus: update with hint to skip input downloads

  chapmanb

  committed
  b0d68dc

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Commits on Dec 7, 2017

• DNAnexus: allow empty arrays for inputs

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  chapmanb

  committed
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Commits on Dec 6, 2017

• Update DNAnexus CWL workflow with vrn_file support

  chapmanb

  committed
  a95a9d3

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Commits on Dec 3, 2017

• vrn_file support for somatic and gVCF workflows

  chapmanb

  committed
  67bbbaf

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Commits on Nov 15, 2017

• Improvements to SV call and parallelization

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  chapmanb

  committed
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Commits on Nov 6, 2017

• Small test for DNAnexus integration

  chapmanb

  committed
  54c3abc

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Commits on Oct 20, 2017

• Generalize coverage estimation and CNV calls

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  chapmanb

  committed
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Commits on Oct 14, 2017

• Somatic and joint: mosdepth general coverage

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  chapmanb

  committed
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Commits on Oct 2, 2017

• Pass resources and more multicore variantcall

  chapmanb

  committed
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Commits on Oct 1, 2017

• Multicore variant calling + strelka2 in tests

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  chapmanb

  committed
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Commits on Sep 22, 2017

• Add test set for SV calling

  chapmanb

  committed
  835cb68

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Commits on Sep 21, 2017

• New space estimates + strelka2 tests

  chapmanb

  committed
  7f1e290

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Commits on Sep 6, 2017

• Remove SV testing work from somatic CWL

  chapmanb

  committed
  51012ac

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