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"
• --tar-rawdata-for-download : tar a rawdata dir and place it in $location, cuz downloading multiple single files over ssh has horrible performance

[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

________________________________ 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 <RunID>/ --remove-demux <RunID> / --remove-fortransfer <RunID> / --(re)upload-nird <RunID> / --(re)upload-vigasp <RunID> (Issue #60) I am lacking context here? — Reply to this email directly, view it on GitHub<#60 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ASS7CRBUPGDKB2NXTIXITADXE73GHANCNFSM6AAAAAAXYJHK74>. You are receiving this because you were assigned.Message ID: ***@***.***>

[georgemarselis-nvi]

demultiplexctl --(un)mark-bad / --(un)mark-control / --mark-good