Bugfixes for Python 3
sebastian-luna-valero
released this
17 Nov 11:29
·
87 commits
to master
since this release
- 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