Version 0.4.0
- Add mark-duplicates step - #40.
- Convert existing samtools commands in templates to corresponding available sambamba one - #41.
- Add bamStats process - #42
- Add process and logic to download input files - #43
- Support compressed reference files - #44
- Replace groupBy related logic in pipeline script - #46
Additional fixes and improvements
- Add memory limit to sambamba sort command in RSEM quantification step
- Add sort buffer size option in sambamba markdup
- Update container for fetch process
- Update IHEC profile BAM sorting tool
- Update Nextflow and TravisCI config files
- Update gem mapping templates for new version of samtools
- Add nextflow config profiles for IHEC and update TravisCI configuration
- Clean-up into calls using closure syntax
- Set halfCpus as integer and fix it when task.cpus is 1
- Add Dockerfiles
- Update readme and add description of pipeline parameters
- Add Singularity section to readme with tips and troubleshoot
- Update tool versions in readme
- Bump sambamba version to 0.7.0
- Bump tool versions for bamstats, samtools and RSeQC
Full Changelog: v0.3.0...v0.4.0