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BU-ISCIII / buisciii-tools

set of helper tools for bu-isciii management of its core services portfolio.
GNU General Public License v3.0
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Files that should be included in clean process for rna-seq template #199

Closed Shettland closed 4 months ago

Shettland commented 8 months ago

Aligned.out.bamand Aligned.toTranscriptome.out.bam are intermediate files for each sample that are generated during rna-seq's nextflow pipeline but are not used in later processes of the service. The size of these files is ussually enough to be taken into consideration for removal during cleaning of the folders.

I'd recommend adding to "files" in https://github.com/BU-ISCIII/buisciii-tools/blob/main/bu_isciii/templates/services.json:

https://github.com/BU-ISCIII/buisciii-tools/blob/3accca9be01a9c9a5c07ebc7f63e771c91968ccf/bu_isciii/templates/services.json#L139-L150

saramonzon commented 7 months ago

@Shettland I agree, add them to the json in the next PR you prepare! Do you agree @svarona ?

saramonzon commented 7 months ago

Mm reading another issue, if they are big big files we should consider a separate sh script in the lablog for deleting them using srun for now? until we revisit the clean module to see if we can include a srun deletion process

svarona commented 7 months ago

Aligned.toTranscriptome.out.bam might be needed in case of differential expressed transcripts? Maybe it would be better a custom script from which we could delete Aligned.toTranscriptome.out.bam or any other .bam in specific cases so they won't be deleted.

jaimeozaez commented 4 months ago

Done. Files set in services.json file and they will be removed from rnaseq services when clean module runs.