Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Mirrors
biopet.biopet
Commits
ff41dff0
Commit
ff41dff0
authored
Jan 27, 2017
by
Peter van 't Hof
Browse files
Added release notes
parent
9867341f
Changes
1
Hide whitespace changes
Inline
Side-by-side
docs/releasenotes/release_notes_0.8.0.md
0 → 100644
View file @
ff41dff0
# Release notes Biopet version 0.8.0
### Highlights
*
Biopet is now fully hosted at github.
*
Several major improvements on using Centrifuge for metagenomics data analysis
*
Added XHMM as a tool for copy number analysis
*
Added support for SLURM
*
Added tool to create a graphical representation of pipeline progress.
*
Added soft clipping metrics to HTML report
## Full change list
### Task
* [BIOPET-508] - Move Biopet completly to github
### Bug
* [BIOPET-337] - Rscript summary from Queue doesn't work
* [BIOPET-353] - Log outputs doesn't contain classname ( ..out issue)
* [BIOPET-369] - cn.mops fails on small chromosomes
* [BIOPET-379] - Biopet error when json file not correctly formated
* [BIOPET-383] - Sample json not checked for invalid libraries
* [BIOPET-384] - Select proper values in VcfWithVcf when when number=A
* [BIOPET-385] - Cannot combine doNotRemove in VepNormalizer with chunked Toucan
* [BIOPET-386] - VcfFilter's mustHaveVariant option ignores certain genotypes
* [BIOPET-394] - Flanking on pysvtools is required
* [BIOPET-403] - Report centrifuge does not display separate library plots when enabled
* [BIOPET-405] - Toucan with custom fields fails
* [BIOPET-409] - CatVariants failing after Delly
* [BIOPET-410] - Krona plots in GearsSingle are not correct for centrifuge
* [BIOPET-415] - SortVcf extensions does not see .tbi file as output
* [BIOPET-418] - Nullpointer when config file is empty
* [BIOPET-450] - Base counts tests are failing
* [BIOPET-458] - Pipeline help status no longer given
* [BIOPET-473] - Dustbin pipeline does not show centrifuge report
* [BIOPET-481] - Chunksize can't go higher then 2G because of limitions a INT
* [BIOPET-485] - files from fifo's from paired-end flexiprep are in the graph
* [BIOPET-486] - BreakdancerCaller does not depend on bam file in graph
* [BIOPET-488] - Bastats does not depend on index of bam file
* [BIOPET-491] - Summary of flexiprep not depens on qc_cmd
* [BIOPET-493] - FastqSplitter is disconnected from the graph
* [BIOPET-495] - Fix XHMM
* [BIOPET-496] - Alignment plot does not show stats
* [BIOPET-504] - Validate vcf step does not have an output file
* [BIOPET-507] - To much file handles for .out files
* [BIOPET-509] - VcfFilter MustHaveVariant does not check if sample exist
* [BIOPET-516] - Config value is not correct for skip_trim and skip_clip
* [BIOPET-526] - bammetrics summary fails with empty histogram array
* [BIOPET-544] - Link to assembly report is broken
### Improvement
* [BIOPET-309] - Colapse output files of vcfstats into 1 file
* [BIOPET-317] - Remove unnecessary intermediate bams to free up more space when pipeline finishes successfully
* [BIOPET-359] - Enable htseq to count multiple-alignments
* [BIOPET-374] - Add clipping stats to html report
* [BIOPET-387] - Convenience methods for semantic versions in Version
* [BIOPET-389] - Shiva is overzealous with sorting amplicon bed files
* [BIOPET-395] - Lazy dict cache in reference module
* [BIOPET-396] - Add support for multiple versions of annotations in config file
* [BIOPET-398] - Change default in Gears to centrifuge
* [BIOPET-406] - Add a better error / exception when output dir is not writable
* [BIOPET-411] - Option to send full fastq file to gears instead of only unmapped reads
* [BIOPET-412] - Make files intermediate in Gears
* [BIOPET-413] - Implementing piping for centrifuge
* [BIOPET-414] - Add all arguments to centrifuge
* [BIOPET-416] - Add stats output of centrifuge
* [BIOPET-426] - Make deps.json run in normal mode
* [BIOPET-463] - Test and update docs GEARS for Centrifuge
* [BIOPET-464] - Implement skip_flexiprep in gears
* [BIOPET-469] - Adding functional testing on XHMM
* [BIOPET-471] - Add agregated stats to BamStats
* [BIOPET-472] - Documentation for XHMM feature
* [BIOPET-475] - Reorganize .log dir
* [BIOPET-477] - Adding refcalls to MpileupToVcf
* [BIOPET-480] - Remove duplicate jobs in bam2wig
* [BIOPET-483] - Add fa.gz / samtools faidx on fa.gz to IndexReference
* [BIOPET-484] - Update documentation for biopet developper
* [BIOPET-489] - Fix compile warnings
* [BIOPET-498] - Add testing for PipelineStatus
* [BIOPET-503] - Colapse output files of bamstats into 1 file
* [BIOPET-506] - Add check if R1 and R2 are the same
* [BIOPET-525] - Adding unassigned reads to Krona plot
* [BIOPET-532] - Add jenkins setup to documentation and README
### New Feature
* [BIOPET-399] - Add walltime to core
* [BIOPET-402] - Tool for filtering fastq files based on read names
* [BIOPET-417] - Config template tools
* [BIOPET-419] - Create Tsv to Samples.yml converter for sample sheet
* [BIOPET-425] - Add main jobs to deps.json
* [BIOPET-427] - Crompress deps.json with only main jobs
* [BIOPET-428] - Generate a dot file with only main jobs
* [BIOPET-460] - Vcf/dbsnp validate step
* [BIOPET-466] - Write XHMM wrappers
* [BIOPET-467] - Write XHMMMethod in Shiva
* [BIOPET-468] - XCNV to BED conversion tool
* [BIOPET-470] - Implement DepthOfCoverage wrapper
* [BIOPET-476] - Tool to check for status of pipeline
* [BIOPET-497] - Add status to compressed plot
* [BIOPET-500] - Add support for Slurm
* [BIOPET-421] - Implement XHMM
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment