v0.6.1

0.6.1 (2025-12-09)

Bug Fixes

• aviti run name (#255) (8902836)

v0.6.0

0.6.0 (2025-10-09)

Features

• Reorganized statistics into specific sample folders. (07d51ef)
• scATAC, dual index, lanesplitting support for AVITI (#250) (07d51ef)

Bug Fixes

• updated optical duplicate parameters for Aviti. (07d51ef)
• Updated SAMBA integration for Aviti. (07d51ef)

v0.5.1

0.5.1 (2025-10-07)

Bug Fixes

• release wd40 for double digit seq_dir ints (#248) (0b42642)

v0.5.0

0.5.0 (2025-10-06)

Features

• try release please (#246) (51f66fd)

Release 0.4.2

What's Changed

• Contam burkhold by @WardDeb in #238
• Fix how the aviti flag is passed between funcitons by @katsikora in #240
• Format sequencing data volume path generation by @katsikora in #242
• cleanup aviti flag usage + contaminome by @katsikora in #241

Full Changelog: v0.4.1...v0.4.2

Release 0.4.1

What's Changed

• flowcell name checks aviti by @WardDeb in #230
• Newflowcell by @WardDeb in #231
• deal with 4 -> 1 phiX mapping by @WardDeb in #232
• until better defined, assume dualIx and PE by default by @WardDeb in #233
• Lane splitting ks by @katsikora in #234
• barcode masking and mismatches by @katsikora in #235
• Aviti by @katsikora in #236

Full Changelog: v0.4.0...v0.4.1

karl

What's Changed

• Added pseudomonas-fluorescens and pseudomonas-yamanorum to the custom… by @gerikson in #216
• pytest updates by @WardDeb in #217
• Aviti implementation by @WardDeb in #222
• drop os. for path handling by @WardDeb in #223
• Threading by @WardDeb in #227
• deal with PosixPath in kraken runner by @WardDeb in #224
• escape runCompletion for aviti runs by @WardDeb in #228
• Aviti, threading, pathlib by @WardDeb in #229

New Contributors

• @gerikson made their first contribution in #216

Full Changelog: v0.3.2...v0.4.0

v0.3.2

Change to deal with parkour organism returning [name, label, yaml].
String in e-mail isn't split, try - except to handle none-types (project not tracked under FID in parkour).
contamination screen includes s.pombe

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.