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@sebastian-luna-valero sebastian-luna-valero released this 25 May 08:32
· 7 commits to master since this release
v0.3.3
46f3840
  • Updated documentation for pipeline_readqc tutorial; #386
  • Updated multiqc to 1.4 in conda environment ; #389
  • pipeline_mapping: merge bam files as part of the full target; #384
  • fix Cluster.py for PBSpro ; #385
  • pipeline_peakcalling: produce normalised BigWigs if the samples are generated using the quantitative ChIP-seq method ; #382
  • pipeline_readqc: bugfix trim_galore pre-processing ; #391
  • Control module in Pipeline.py: bugfix the PBSpro connection ; #390
  • pipeline_enrichment: bugfix runGsea task in pipeline_enrichment ; #392
  • Cluster module in Pipeline.py: bugfix the job submission in SGE with an empty queue parameter ; #393
  • pipeline_bamstats: changed way bam files are imported ; #395
  • pipeline_exome: fix import of PipelineExomeAncestry ; #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 ; #399
  • make threads=1 instead of threads=10 for build_report in pipeline.ini ; #401
  • fix memory requirements for pipeline_genesets ; #402
  • update docs to clarify expected fastq name for input files ; #403
  • replace pipeline_annotations with pipeline_genesets in quickstart ; #405
  • update report for bamstats ; #404
  • add back explicit reporting of failed cluster jobs ; #406
  • use cgat gtf2tsv -f in pipeline_genesets ; #408
  • make sure we stick to conda 4.3 until a workaround is found for conda 4.4 ; #409
  • increase priority of $HOME/.cgat ini file ; #412 ; #414
  • typo in pipeline_bamstats ; #413
  • make sure the job environment is the same when submitting jobs to the cluster or running them locally; #411
  • remove duplicated function ; #416
  • pipeline_exome: update snpEff from 4.1 to 4.3 ; #417
  • separate statements for paired-end and single-end data in CGATPipelines/PipelineRnaseq.py ; #418
  • pipeline_mapping: avoid duplicating entries in loadReadCounts ; #420
  • added pipeline_chiptools ; #379
  • fix cutadapt paired untrimmed command ; #423
  • pipeline_readqc: disable fastq_screen by default ; #422
  • update conda from 4.3 to 4.5 (solving "CXXABI_1.3.9' not found" error ; ContinuumIO/anaconda-issues#5191) ; ebc3b74...3ef1460
  • added test for C/C++ compiler ; #425
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