[Debian-med-packaging] bcbio_1.1.4-1_amd64.changes ACCEPTED into unstable

[Debian FTP Masters]

Accepted:

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Format: 1.8
Date: Thu, 11 Apr 2019 12:56:58 +0200
Source: bcbio
Binary: bcbio bcbio-doc python3-bcbio
Architecture: source all
Version: 1.1.4-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Changed-By: Steffen Moeller <moeller at debian.org>
Description:
 bcbio      - toolkit for analysing high-throughput sequencing data
 bcbio-doc  - Documentation for RNAseq-workflows of bcbio(-nextgen)
 python3-bcbio - library for analysing high-throughput sequencing data
Changes:
 bcbio (1.1.4-1) unstable; urgency=medium
 .
   * New upstream release.
     - Move to Python 3.6. A python2 environment in the install runs
       non python3 compatible programs. The codebase is still compatible
       with python 2.7 but will only get run and tested on python 3 for
       future releases.
     - RNA-seq: fix for race condition when creating the pizzly cache
     - RNA-seq: Add Salmon to multiqc report.
     - RNA-seq single-cell/DGE: Properly strip transcript versions from
       GENCODE GTFs.
     - RNA-seq: Faster and more flexible rRNA biotype lookup.
     - Move to R3.5.1, including updates to all CRAN and Bioconductor
       packages.
     - tumor-only germline prioritization: provide more useful germline
       filtering based on prioritization INFO tag (EPR) rather than filter
       field.
     - Install: do not require fabric for tool and data installs, making
       full codebase compatible with python 3.
     - variant: Filter out variants with missing ALT alleles output
       by GATK4.
     - GATK: enable specification of spark specific parameters with
       `gatk-spark` resources.
     - RNA-seq single-cell/DGE: added `demultiplexed` option. If set to
       True, treat the data as if it has already been demultiplexed into
       cells/wells.
     - Multiple orders of magnitude faster templating with thousands of
       input files.
 .
   * Moved stringtie from suggested to recommended
   * Added dependency on xonsh for testing
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Files:
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