v0.3.1

• wolbachia / staph aureus included in contamination
• docs requirements
• wd40 cleanup

Ludwig (der Jüngere)

• Sanitate parkour organisms
• parkour fex status updates upon release
• properly capture disk quota errors
• properly take Q30 into account
• Pre-existing BCLConvert logs get purged
• pbr dropped in favor of scm, linting moved to ruff
• workflow oriented around flowcellClass, flowcell 'walks' now possible.
• Documentation is updated
• Logging structure somewhat harmonized
• moved over to pathlib over os.path, although this isn't finished yet.

v0.2.8

• Requires the MultiQC version 1.21 or later
• fetchLatestSeqDir function from misc.py was updated to detect the latest sequencing_data volume from PI directory.

v0.2.7

• emailProjectFinished.py now populates parkour 'put_filepaths' API endpoint with the data location (subsequently, parkour also sets statuses from 'sequenced' to 'delivered')
• Dependencies were updated. Ruamel API deprecated an odd behavior on how YAML was dumped, this was adjusted now.
• Subject for emails take a config value now, so that dissect test runs can be discerned easily.
• We don't use userList.txt anymore, instead we get user contact details from Parkour API
• Configuration of Parkour was simplified (just 1 URL)
• Lanesplit checks on sampleIDs (rather than samplenames), so it's lane-aware now.
• split up zebrafish contamination into mito - rrna - zebrafish

v0.2.6

• improve logger
• miseq req depths override
• sanitize spaces in sample names

validateMiSeq

• MiSeq runs are validated for runcompletionstatus
• new seqfac dir nested structure

autoP5

• Purge apostrof
• Auto P5 reverse complement in case of MiSeq runs (only if the full flow cell is bad)

colliders

• deal with omitted colliding samples
• discriminate non-omitted empty vs omitted in email / mqc report
• escape included projects not present in the FID in parkour
• boost flake/precommit
• scATAC protocol name changes + tests for masking them
• project returns in the email are only those of the lane(s).

v0.2.2: bugfixes (#127)

• sanitize é in user / PI names.
• fex uploads can be disabled in the config
• mismatch changes in the demuxsheet are reflected in the email + mqc report as well.

v0.2.1

• updated tests.
• allow empty kraken reports for email.