Published May 25, 2018
| Version v0.3.3
Software
Open
CGATOxford/CGATPipelines: Bugfixing release
Authors/Creators
- Andreas Heger1
- Sebastian Luna-Valero2
- Tom Smith
- Ian Sudbery3
- MikeDMorgan
- Jakub Scaber
- Check your git settings!
- Nick Ilott
- jethro
- Steve Sansom4
- Charlie-George
- Adam Cribbs
- Tim-HU
- Antonio5
- KatyBrown
- Reshma
- nsahgal
- logust79
- Alice Mayer
- zahra-aboukhalil
- Matthew Parker
- jencyw
- Kevin Rue-Albrecht6
- jaime11
- Hania J Pavlou6
- BilyanaStoilova
- 1. MRC
- 2. CGAT
- 3. University of Sheffield
- 4. Kennedy Institute of Rheumatology, University of Oxford
- 5. Imperial College London
- 6. University of Oxford
Description
- Updated documentation for pipeline_readqc tutorial; https://github.com/CGATOxford/CGATPipelines/pull/386
- Updated multiqc to 1.4 in conda environment ; https://github.com/CGATOxford/CGATPipelines/pull/389
- pipeline_mapping: merge bam files as part of the full target; https://github.com/CGATOxford/CGATPipelines/pull/384
- fix Cluster.py for PBSpro ; https://github.com/CGATOxford/CGATPipelines/pull/385
- pipeline_peakcalling: produce normalised BigWigs if the samples are generated using the quantitative ChIP-seq method ; https://github.com/CGATOxford/CGATPipelines/pull/382
- pipeline_readqc: bugfix trim_galore pre-processing ; https://github.com/CGATOxford/CGATPipelines/pull/391
- Control module in Pipeline.py: bugfix the PBSpro connection ; https://github.com/CGATOxford/CGATPipelines/pull/390
- pipeline_enrichment: bugfix runGsea task in pipeline_enrichment ; https://github.com/CGATOxford/CGATPipelines/pull/392
- Cluster module in Pipeline.py: bugfix the job submission in SGE with an empty queue parameter ; https://github.com/CGATOxford/CGATPipelines/pull/393
- pipeline_bamstats: changed way bam files are imported ; https://github.com/CGATOxford/CGATPipelines/pull/395
- pipeline_exome: fix import of PipelineExomeAncestry ; https://github.com/CGATOxford/CGATPipelines/pull/397
- pipeline_rnaseqdiffexpression: small change to avoid confusion when running featurecounts ; https://github.com/CGATOxford/CGATPipelines/pull/398/files
- pipeline.py: prevent pipelines from running when DRMAA is not available ; https://github.com/CGATOxford/CGATPipelines/pull/399
- make threads=1 instead of threads=10 for build_report in pipeline.ini ; https://github.com/CGATOxford/CGATPipelines/pull/401
- fix memory requirements for pipeline_genesets ; https://github.com/CGATOxford/CGATPipelines/pull/402
- update docs to clarify expected fastq name for input files ; https://github.com/CGATOxford/CGATPipelines/pull/403
- replace pipeline_annotations with pipeline_genesets in quickstart ; https://github.com/CGATOxford/CGATPipelines/pull/405
- update report for bamstats ; https://github.com/CGATOxford/CGATPipelines/pull/404
- add back explicit reporting of failed cluster jobs ; https://github.com/CGATOxford/CGATPipelines/pull/406
- use cgat gtf2tsv -f in pipeline_genesets ; https://github.com/CGATOxford/CGATPipelines/pull/408
- make sure we stick to conda 4.3 until a workaround is found for conda 4.4 ; https://github.com/CGATOxford/CGATPipelines/pull/409
- increase priority of $HOME/.cgat ini file ; https://github.com/CGATOxford/CGATPipelines/pull/412 ; https://github.com/CGATOxford/CGATPipelines/pull/414
- typo in pipeline_bamstats ; https://github.com/CGATOxford/CGATPipelines/pull/413
- make sure the job environment is the same when submitting jobs to the cluster or running them locally; https://github.com/CGATOxford/CGATPipelines/pull/411
- remove duplicated function ; https://github.com/CGATOxford/CGATPipelines/pull/416
- pipeline_exome: update snpEff from 4.1 to 4.3 ; https://github.com/CGATOxford/CGATPipelines/pull/417
- separate statements for paired-end and single-end data in CGATPipelines/PipelineRnaseq.py ; https://github.com/CGATOxford/CGATPipelines/pull/418
- pipeline_mapping: avoid duplicating entries in loadReadCounts ; https://github.com/CGATOxford/CGATPipelines/pull/420
- added pipeline_chiptools ; https://github.com/CGATOxford/CGATPipelines/pull/379
- fix cutadapt paired untrimmed command ; https://github.com/CGATOxford/CGATPipelines/pull/423
- pipeline_readqc: disable fastq_screen by default ; https://github.com/CGATOxford/CGATPipelines/pull/422
- update conda from 4.3 to 4.5 (solving "CXXABI_1.3.9' not found" error ; https://github.com/ContinuumIO/anaconda-issues/issues/5191) ; https://github.com/CGATOxford/CGATPipelines/compare/ebc3b7478b774...3ef14607e91b7
- added test for C/C++ compiler ; https://github.com/CGATOxford/CGATPipelines/pull/425
Files
CGATOxford/CGATPipelines-v0.3.3.zip
Files
(5.6 MB)
| Name | Size | Download all |
|---|---|---|
|
md5:40aa902f9fe1cc0cef0ffedfb8b4a32e
|
5.6 MB | Preview Download |
Additional details
Related works
- Is supplement to
- https://github.com/CGATOxford/CGATPipelines/tree/v0.3.3 (URL)