Add --only_step options
IStevant opened this issue · comments
Description of feature
Hi!
in the cutandrun pipeline, I really appreciate the option to run only one part of the pipeline such as --only_alignment to stop just after mapping the data.
Would it be possible to implement something similar for the chipseq pipeline?
My usage: I am running the chipseq pipeline on cutandrun data because single-end reads are not supported in the cutandrun pipeline. My data contain E.coli spike-ins that I would like to quantify in the exact same condition the samples are processed. If I run the pipeline on the E.coli genome just to quantify the E.coli reads, the pipeline fails while some samples are still mapping because the first sample to finish the mapping goes for peak calling which obviously fails due of the law amount of reads. As such, I have to re-run the pipeline on the unfinished samples again to until all samples are eventually mapped.
If an --only_alignment option existed, I could map my spike-ins and stop before the peak calling.