Comments (1)
This is being handled in the refactor branch
from automate_demultiplex.
Related Issues (20)
- Remove SWIFT HOT 2
- newline in congenica run commands file required
- This should not be using append mode HOT 1
- Implement an exponential backoff strategy for retries when uploading to DNA Nexus
- Remove any emails from list and instead store in a separate configuration file on the workstation
- Add note that when this repo is updated the following repos also require update HOT 1
- Add fastq checks prior to upload HOT 2
- Add class to logger module that counts number of error and warning log messages
- Switch hard coded paths to cmd line inputs
- Do we want to send samples being processed emails to rest of teams HOT 1
- Remove WES and SNP
- Remove all hardcoded paths / secrets as env variables / a configuration service HOT 1
- Use tmp_path / tmp_factory_path in testing temp files
- Disable syslog in logging HOT 1
- Look at usage of sys.exit(1)
- Fix this HOT 1
- Automate upload of development runs
- Upgrade upload agent
- Move pipelineemails into separate module - ad_email?
- Issue with demultiplexing for specific run folder with -r flag
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