Not to copy unnecessary files to results dir

[sk-sahu]

• [x] trimmed files - only keep logs
• [x] copy .bw only once - all of them into the single folder
• [x] trimmed FastQCs in QC folder - all this information is available in the MultiQC
• [ ] remove the duplicated MultiQC file (keep the renamed one)
• [ ] bam files - can we figure out a way to zip this folder? Would that help with space?
• [ ] unmapped file - making a param if a user want to generate those files. somewhere here
• [ ] Can we zip the folders with the merged gtf here?

[sk-sahu]

Removing trimmed file already implemented in https://github.com/TheJacksonLaboratory/splicing-pipelines-nf/pull/219

[angarb]

@sk-sahu , after speaking with @olgaanczukow, 1) In the QC folder, can we remove the trimmed QC files and keep the raw QC files? Can we zip the folder containing the raw QC files? The raw QC files have some information that complements the MultiQC. 2) We do probably need to keep the bams (especially on the cluster) - however, is there a way to also compress this star_mapped folder? 3) For now, we probably do need to keep the merged folder - can we also compress this folder?

[sk-sahu]

remove the duplicated MultiQC file (keep the renamed one)

CloudOS will be able to parse the original MultiQC files name - multiqc_report.html to show on the multiqc tab, So need to keep both. Also, these are very big.

[angarb]

@sk-sahu where are the trimmomatic logs going? I can't seem to find that folder

[sk-sahu]

@angarb Agree now they are not being published - https://github.com/TheJacksonLaboratory/splicing-pipelines-nf/blob/51f6473475a11b169524f04caaf7b404f3b1e3bb/main.nf#L479-L488

Will fix this

[Vlad-Dembrovskyi]

created separate issues for pending tasks. closing this one.