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Issues list

Automate upload of development runs
#537 opened May 29, 2024 by RachelDuffin
Fix this
#534 opened May 1, 2024 by RachelDuffin
Look at usage of sys.exit(1)
#533 opened Apr 23, 2024 by RachelDuffin
Disable syslog in logging
#532 opened Mar 4, 2024 by RachelDuffin
Use tmp_path / tmp_factory_path in testing temp files
#531 opened Mar 4, 2024 by RachelDuffin
Remove all hardcoded paths / secrets as env variables / a configuration service
#530 opened Mar 4, 2024 by RachelDuffin
1
Remove WES and SNP
#529 opened Feb 21, 2024 by RachelDuffin
Do we want to send samples being processed emails to rest of teams
#528 opened Feb 7, 2024 by RachelDuffin
Switch hard coded paths to cmd line inputs
#527 opened Feb 6, 2024 by RachelDuffin
Add class to logger module that counts number of error and warning log messages
#526 opened Feb 2, 2024 by RachelDuffin
Add fastq checks prior to upload
#521 opened Dec 14, 2023 by RachelDuffin
1
Add note that when this repo is updated the following repos also require update
#519 opened Nov 30, 2023 by RachelDuffin
1
Remove any emails from list and instead store in a separate configuration file on the workstation
#518 opened Nov 23, 2023 by RachelDuffin
Implement an exponential backoff strategy for retries when uploading to DNA Nexus
#516 opened Nov 13, 2023 by Graeme-Smith
This should not be using append mode
#515 opened Oct 31, 2023 by RachelDuffin
1
Remove SWIFT
#509 opened Oct 20, 2023 by RachelDuffin
1
Remove mokaamp
#508 opened Oct 20, 2023 by RachelDuffin
1
replace Viapath with GSTT (future proof incase KCL can also use these scripts)
#505 opened Sep 22, 2023 by aledj2
add HRD and OKD to list of allowed prefixes (maybe more?)
#503 opened Sep 8, 2023 by aledj2
Having None here results in stderr when executing dx run commands. Can this be changed to something else?
#502 opened Aug 29, 2023 by aledj2
logfile list might be empty, eg if copy of failed integrity check
#497 opened May 24, 2023 by aledj2
Change upload_agent_script_logfiles directory to match name of logfiles stored within it
#481 opened Mar 20, 2023 by RachelDuffin
1
Move email template string to an actual template in a templates directory
#480 opened Mar 20, 2023 by RachelDuffin
1
Refactor upload and setoff workflows script and add test suite
#479 opened Mar 16, 2023 by RachelDuffin
1
Create a github actions page that can be accessed by both the team / other teams
#474 opened Feb 13, 2023 by RachelDuffin
ProTip! Follow long discussions with comments:>50.