Add no_bigwigs rule to run only quantification and alignment but not deepTools bamCoverage.
Change the default minute run behavior to running minute without plotFingerprint (this is reflected also on the multiqc_report.htmlfile names). I see it as a related change towards less waste of computation time.
In some cases (esp. as multiplexing go high and we have a lot of libraries with fewer reads on them) we are more interested in the global quantification than in the bigWig files. On top of that, making the bigWig files with bamCoverage is far from cheap regardless of BAM file size (see #89).
One can always run the bigWig generation afterwards without needing to re-run the previous steps, so I think this also goes a long way towards a smarter use of computation resources. So if one would want to generate bigWig files afterwards, the approach would be minute run no_bigwigs and later on minute run on the same directory.
Since this modification is in the spirit of a faster quantification and makes the most sense for lower coverage BAM files, no_bigwigs also excludes the fingerprint plots.
Small PR to allow (and prefer) faster runs:
no_bigwigsrule to run only quantification and alignment but notdeepTools bamCoverage.minute runbehavior to runningminutewithoutplotFingerprint(this is reflected also on themultiqc_report.htmlfile names). I see it as a related change towards less waste of computation time.In some cases (esp. as multiplexing go high and we have a lot of libraries with fewer reads on them) we are more interested in the global quantification than in the bigWig files. On top of that, making the bigWig files with
bamCoverageis far from cheap regardless of BAM file size (see #89).One can always run the bigWig generation afterwards without needing to re-run the previous steps, so I think this also goes a long way towards a smarter use of computation resources. So if one would want to generate bigWig files afterwards, the approach would be
minute run no_bigwigsand later onminute runon the same directory.Since this modification is in the spirit of a faster quantification and makes the most sense for lower coverage BAM files,
no_bigwigsalso excludes the fingerprint plots.