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Commits on Nov 21, 2017
  1. Coverage: fixes for skipping coverage assessment

    chapmanb committed Nov 21, 2017
    Correctly skip coverage and return original items if not running CNV
    callers.
Commits on Nov 20, 2017
  1. Remove GATK read backed phasing support

    chapmanb committed Nov 20, 2017
    GATK4 removes ReadBackedPhasing and now recommend using phasing in
    GATK HaplotypeCaller:
    
    https://gatkforums.broadinstitute.org/gatk/discussion/45/purpose-and-operation-of-read-backed-phasing
    
    This removes the older functionality which was causing problems. Fixes #2158
  2. Fix bug with GATK Haplotype RNA-seq variant calls

    chapmanb committed Nov 20, 2017
    Split collapsed samples for GATK HaplotypeCaller joint calling back
    into individual samples. Fixes #2162
  3. CNV: avoid duplicate bins when adding gene names

    chapmanb committed Nov 20, 2017
    bedtools closest creates duplicate lines when finding equally spaced
    features. This chooses the first gene name, avoiding the duplication.
    Fixes #2158
Commits on Nov 19, 2017
  1. SV: initial support for TitanCNA

    chapmanb committed Nov 19, 2017
    Provides wrapper for TitanCNA analysis of tumor/normal somatic CNVs.
    Initial implementation needs testing on real samples to select and
    pass along final selections. Work in progress for #1876
Commits on Nov 18, 2017
  1. Merge pull request #2161 from cure/master

    chapmanb committed Nov 18, 2017
    Fix typos.
Commits on Nov 17, 2017
  1. Fix typos.

    cure committed Nov 17, 2017
  2. strelka2: avoid nested relative symlinks

    chapmanb committed Nov 17, 2017
    Copies output files to avoid symlink issues running with CWL on
    Arvados.
  3. GATK: only use jdk_deflater/inflater for 3.8+

    chapmanb committed Nov 17, 2017
    Non-intel deflater options not present in earlier versions. Fixes #2158
  4. CWL: add arvados requirements as hints; docs

    chapmanb committed Nov 17, 2017
    - Use arvados requirements as hints instead of requirements only
      in arvados environments, making usage more transparent.
    - Improve Arvados running docs.
Commits on Nov 16, 2017
  1. Re-add support for MuTect/old GATK with java7

    chapmanb committed Nov 16, 2017
    Automatic path prepending always used the local java 8 install instead
    of an external java 7 required for MuTect and old GATK versions. This
    avoids using prepended paths for these steps. Fixes #2158
  2. VQSR: use JDK inflater for GATK4 and GATK3

    chapmanb committed Nov 16, 2017
    Avoids ApplyBSQRSpark compression errors seen with GATK4 on
    Docker runs.
Commits on Nov 15, 2017
  1. CWL: only pass arvados hints to arvados CWL

    chapmanb committed Nov 15, 2017
    Other runners like rabix bunny don't like the custom defined
    requirements for Aravdos.
  2. Fixes to get ericscript working.

    roryk committed Nov 14, 2017
    1) simplify call to be more bcbio-like
    2) properly pass number of threads to ericscript
    3) allow manual specification of an ericscript database
  3. CWL: require network access for GATK

    chapmanb committed Nov 15, 2017
    GATK has problems setting up log4j in Docker containers without
    network access. The enables access using the custom arvados requirement
    (https://dev.arvados.org/issues/12593).
  4. CWL: optional SV vrn_file and variantcaller

    chapmanb committed Nov 15, 2017
    Normal samples in tumor/normal pairs do not have associated calls.
    Avoids issues on runners like Toil that check explicitly.
Commits on Nov 14, 2017
  1. Add example template for inDrop singlecell.

    roryk committed Nov 14, 2017
    Partially addresses #2153.
  2. CWL: include normalization in SV calling workflow

    chapmanb committed Nov 14, 2017
    Adds in sv normalization, structuring steps around records instead
    of individual files. Fixes for dealing with records in multiple
    forms of nesting and batched SV calling.
  3. CWL: use linkImports for symlinking with Toil

    chapmanb committed Nov 14, 2017
    Avoid copying files during Toil local runs, instead symlinking.
    Also changes directory run name to `toil_work` to avoid confusion
    with `cwltool_work`.
  4. Merge pull request #2157 from vladsaveliev/dup_qc

    chapmanb committed Nov 14, 2017
    Regroup back samples after processing in heterogeneity module
  5. Regroup back samples after processing in heterogeneity module

    vladsaveliev committed Nov 14, 2017
    Removes redundant normal sample copies for shared normals. Resolves duplicated QC runs for #2154
  6. GATK: correctly apply jdk in/deflater for BQSR

    chapmanb committed Nov 14, 2017
    Apply to problem PrintReads, not BaseRecalibrator. Fixes #2156
  7. Tests: fix unit tests for ericscript

    chapmanb committed Nov 14, 2017
    Avoid calls when ericscript database not present
Commits on Nov 13, 2017
  1. Look up bamsormadup properly.

    roryk committed Nov 13, 2017
    Fixes #2155.