CSI Implementation for Larger Genomes

[emilytrybulec]

Description of feature

Hi,

I've been helping my coworker run this pipeline, but we hit an error with SAMTOOLS_INDEX, which I see isn't that uncommon. Using ext.args, we were able to resolve the error, but only a partial run followed. The last step that ran at that point was MERGED_LIBRARY_MARKDUPLICATES_PICARD, so I was able to git clone and modify the atacseq.nf at line 480 to read
.join(MERGED_LIBRARY_MARKDUPLICATES_PICARD.out.csi, by: [0])

This change allowed for more of the pipeline to run, but it still did not complete. This time, the pipeline was halted at the bam_filter_bamtools.nf subworkflow. I modified line 89 to read
bai = BAM_SORT_STATS_SAMTOOLS.out.csi.mix(SAMTOOLS_INDEX.out.csi) // channel: [ val(meta), [ bai ] ]

These changes allowed for the pipeline to complete using the csi index, and I think it'd be useful to implement these as more global changes. If I didn't have a thorough Nextflow background, I don't think we would be able to use the complete pipeline for this species, so I think making adjustments to allow for easier csi usage would benefit the community as a whole! Let me know if you'd like any additional info!

[JoseEspinosa]

Thanks a lot for your thorough description of your changes, we will incorporate this changes to the pipeline