User story
As a computional biologist casually testing my sample quality, I want to be able to supply bigWig or peak files without needing to have the .bam or .fastq files on hand.
Describe the solution you'd like
The RSeq-CLI should accept bigWig and peak files as input.
Known steps required
[ ] Update process_input.R to accept bigWig and/or peak files as a new argument, preferably with new mode. (e.g., RSeq report -p mypeaks.bed -b mysignal.bw -t 80)
[ ] Allow for output rule in snakemake pipeline to have no bams and either no peaks or no bigWig.
[ ] Update RSeq report module to allow for bigWig/peaks-only input.
[ ] Investigate whether a quality score is still possible from bigWig/peaks only.
[ ] Update usage & detailed usage to reflect changes
[ ] Write relevant unit tests
[ ] Test with publicly-available peak and bigWig files
Additional context
This will require changes to the process_input.R function along with several other components. The snakemake pipeline should still operate as expected.
millerh1
commented
3 years ago
User story As a computional biologist casually testing my sample quality, I want to be able to supply bigWig or peak files without needing to have the .bam or .fastq files on hand.
Describe the solution you'd like The RSeq-CLI should accept bigWig and peak files as input.
Known steps required
RSeq report -p mypeaks.bed -b mysignal.bw -t 80)outputrule in snakemake pipeline to have no bams and either no peaks or no bigWig.Additional context This will require changes to the process_input.R function along with several other components. The snakemake pipeline should still operate as expected.