feature request: add --remove <RunID>/ --remove-demux <RunID> / --rename <RunID>/<Sample> / --remove-fortransfer <RunID> / --(re)upload-nird <RunID> / --(re)upload-vigasp <RunID>

[georgemarselis-nvi]

and relevant functions.

• --remove-demux will remove the demultiplexing directory for that run (and note that in the db by demultiplexed = False
• --remove-fortransfer : will remove the relevant for_transfer directory (and note in the database that the file needs re-uploading?
• --remove-fortransfer : will be the other two combined
• --rename / : renames RunID (and if required and RunID exists, Sample), repackages tar file
• --(re)upload-nird : self-explanatory, tweaks database "transferred-nird = true"
• --(re)upload-vigasp : self-explanatory, tweaks database "transferred-vigasp= true"

[karinlag]

I am lacking context here?

[georgemarselis-nvi]

the idea is that instead of going by hand and deleting a demultiplex/for_transfer/upload folder and/or file, the script does that for you. you don't need to know what runs exist, you can just --list them. helps us command-line folks to locate a run much faster.

that way, we can re-demultiplex/re-transfer files by either knowing the RunID or by --list -ing them. it is essentially data management for the data via the demultiplexing script. it will get there in the future.

it's a neat idea but it is for later.

Best Regards,

---

George Marselis

Linux Engineer

HPC and Bioinformatics @NVI

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From: Karin Lagesen @.***> Sent: Sunday, May 7, 2023 9:41:23 PM To: NorwegianVeterinaryInstitute/DemultiplexRawSequenceData Cc: Marselis, George; Assign Subject: Re: [NorwegianVeterinaryInstitute/DemultiplexRawSequenceData] feature request: add --remove / --remove-demux / --remove-fortransfer / --(re)upload-nird / --(re)upload-vigasp (Issue #60)

I am lacking context here?

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