Commit ff41dff0 authored by Peter van 't Hof's avatar Peter van 't Hof

Added release notes

parent 9867341f
# 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
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