Avoid filename truncation in dupradar.r (+remove detectcores)

SciLifeLab / NGI-RNAseq

Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.

https://ngisweden.scilifelab.se/

MIT License

51 stars 42 forks source link

Avoid filename truncation in dupradar.r (+remove detectcores) #201

Closed rfenouil closed 6 years ago

rfenouil commented 6 years ago

Changed the method to generate basename from input_bam file name.
- Previous method prevented the use of dots in bam filename (truncation of file name at first dot).
Added file.exists checks for bam and gtf files with error message (+bam file must have .bam extension).
Used basename instead of full bam filename for _duprateExpDens.pdf output (to be consistent with other outputs)

rfenouil commented 6 years ago

Sorry I did not mean to commit nbThreads modification into this PR (but still experimenting with github functionalities)... Point of last 2 commits is to avoid the use of detectCores() function by adding a mandatory parameter to dupradar.r script, then use it with nextflow task.cpus process directive.

ewels commented 6 years ago

Looks good to me! @rfenouil - could you add to the CHANGELOG.md file please? Also add yourself to the credits on README.md.

@Hammarn - would be great if you could run a quick test on this on UPPMAX to check that the results are still comparable on a proper run.