Accepted bcbio 1.1.4-1 (source all) into unstable
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Hash: SHA256
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@lists.alioth.debian.org>
Changed-By: Steffen Moeller <moeller@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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