Bugfixing release

• 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

Bugfixing and refactoring release

• removed GCProfile calls from pipelines; #368
• updated installation; #370, #371, #372, #375, #377
• pipeline_readqc.py: call cgat script with cgat command; #374
• PipelineMapping.py: fix so star will work with muti QC; #376
• code changes for improved portability of pipelines; #380
• create Python 2 environments for legacy dependencies; #381
• re-factored pipeline_annotations and pipeline_mappinginto pipeline_genesets and pipeline_bamstats respectively; #373

Bugfixes for Python 3

• fixes for building the docs
• pipeline_peakcalling: changed default blacklist path; #345
• pipeline_peakcalling: bedGraphToBigWig in new environment requires sorted input; #346
• pipeline_peakcalling: debugging for python 3 in peakcalling notebook reports and changing default format to python 3; #347
• added scripts to help find R and Python dependencies: scripts/cgat_deps_R.sh, scripts/cgat_deps_python.sh
• pipeline_peakcalling: added an additional plotting function to generate summary plots after IDR; #348
• pipeline_peakcalling: redirected optimal peaks and conservative peaks to filtered IDR output; #349
• pipeline_rnaseqqc: added functions to check the strandedness of the library, which is required as an input for various mappers; #351
• remove unused imports with autoflakes; #354
• bugfix the way bowtie2 index folder is configured in pipeline_mapping; #356 and #361
• bowtie should not use the quite option so multiqc reports properly; #357
• pipeline_peakcalling: minor bugfix; #358
• pipeline_peakcalling: update to work with sicer in a Python 2 environment ; #359
• added cgatflow command; #360
• updated documentation and moved unused code to obsolete folder; #362
• updated installation; #363 ; #367
• pipeline_peakcalling: update the way IDR is called so it is included as a conda dependency ; #364

First release in Python 3

First version of the code working in Python 3 only.

Last release in Python 2

This is the last version of the code working in Python 2. Next releases will be working in Python 3 only.