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Commits on Jun 21, 2018
Commits on Jun 20, 2018
  1. Fix typo in except clause

    chapmanb committed Jun 20, 2018
Commits on Jun 18, 2018
Commits on Jun 16, 2018
  1. Ansible: update AWS launch script

    chapmanb committed Jun 16, 2018
    - Larger instance types to support Docker rebuilds
    - Support for condor to enable local Cromwell runs
    - Support for dotnet for Pisces support
Commits on Jun 14, 2018
  1. samtools: Add AD to mpileup outputs

    chapmanb committed Jun 14, 2018
    Fixes #2416
Commits on Jun 13, 2018
  1. VerifyBamID: work around issue with extra sample newline

    chapmanb committed Jun 13, 2018
    Works around issue with parsing sample name from BAM file when SM tag is at the
    end of the RG line: Griffan/VerifyBamID#10  Fixes bcbio/bcbio-nextgen#2417
Commits on Jun 12, 2018
  1. CWL: ensure rgnames__sample is part of output step

    chapmanb committed Jun 12, 2018
    Handles cases where runners expect some processing of inputs, even though
    this is really just a pass through of the names. This makes sure they
    are present for all workflows, including QC only.
Commits on Jun 11, 2018
Commits on Jun 10, 2018
Commits on Jun 9, 2018
  1. QC: support VerifyBamID2 for contamination detection

    chapmanb committed Jun 9, 2018
    Initial support for VerifyBamID2 as part of QC. Calculates FREEMIX sequence
    only score using 1000 genomes background and reports in MultiQC report per
    sample.
Commits on Jun 8, 2018
Commits on Jun 7, 2018
  1. RNA-seq variant calling: correct filtering with tools_off: [gatk4]

    chapmanb committed Jun 7, 2018
    Correctly use GATK4 for filtering step after GATK3 variant calling
    with `tools_off: [gatk4]` #2410
Commits on Jun 6, 2018
  1. Merge pull request #2411 from matthdsm/patch-1

    chapmanb committed Jun 6, 2018
    CWL: cromwell torque "check-alive" fix
Commits on Jun 5, 2018
  1. RNA-seq variant calling: add annotation of output VCFs

    chapmanb committed Jun 5, 2018
    Enable annotation of RNA-seq variant calls with same approach as used for
    standard variant calling: vcfanno plus allowing custom input scripts.
  2. CWL: avoid race conditions during multicore BED prep

    chapmanb committed Jun 5, 2018
    Pass in pre-merged variant BED file (`variant_regions_merged`) to avoid
    potential race conditions when running multicore single core jobs. Provide
    standard interface for retrieving from multiple callers with and without
    merging.
Commits on Jun 4, 2018
  1. CWL: add run_number target for manual CWL update

    chapmanb committed Jun 4, 2018
    Enables forcing re-run of completed steps if there are problems or code updates
    by updating a run CWL.
  2. CWL: consistent generation of reference genome_context

    chapmanb committed Jun 4, 2018
    Matches remote changes in bcbio-vm to provide consistently ordered
    outputs in samples.json.
Commits on Jun 3, 2018
  1. Improve handling of multi-normal batch samples

    chapmanb committed Jun 3, 2018
    Ensure single elements for samples shared by multiple normal batches
    during tumor/normal paired. Thanks to @ohofmann.
  2. CWL: support for UMIs with merging, minimap and bbmap

    chapmanb committed Jun 3, 2018
    - Ensure umi_bam files get handled consistently with align_bam to avoid
      list/single BAM errors with CWL runs.
    - Allow UMIs with minimap2 and bbmap by correctly handling file extensions.
  3. Improve ansible startup script for Google Compute

    chapmanb committed Jun 3, 2018
    - Control boot disk size to avoid small inputs
    - Better wait for SSH startup
    - Add in Docker, Condor and dotnet for validation testing
Commits on Jun 2, 2018
Commits on Jun 1, 2018
  1. peddy: support hg38; avoid ensemble calling issues

    chapmanb committed Jun 1, 2018
    - Adds support for hg38 with peddy. brentp/peddy#44
    - Capture low overlap failures during PCA analysis, skipping peddy run
    - Avoids using ensemble inputs for peddy, instead preferring single caller
      outputs. bcbio/bcbio-nextgen#2384
  2. CWL: fix SV coverage errors when CNVkit not enabled

    chapmanb committed Jun 1, 2018
    Avoids problematic outputs when missing CNVkit (and thus not calculating some
    coverage metrics for CNV calling). Fixes #2406
Commits on May 31, 2018
Commits on May 30, 2018
  1. Merge pull request #2407 from matthdsm/patch-1

    chapmanb committed May 30, 2018
    cromwell: torque qsub fix
Commits on May 29, 2018
  1. RNA-seq variant calling: parallel by regions

    chapmanb committed May 29, 2018
    Expand previous parallel by chromosome to parallel by regions to avoid memory
    and incorrect outputs with GATK HaplotypeCallerSpark (#2375). We now split
    by region blocks trying to avoid very large regions as a way to mitigate
    memory requirements and problematic VCF outputs.
Commits on May 28, 2018
  1. RNA-seq: fastq quality conversion without trim

    chapmanb committed May 28, 2018
    Ensures conversion of quality scores via groom if we don't have trimming
    enabled (since trim also converts quality scores as part of a single process).
    Fixes #2404
Commits on May 27, 2018
  1. CWL: improve Cromwell scaling on large sample sizes

    chapmanb committed May 27, 2018
    Provide more memory for runner and longer timeout for
    filesystem database reads.