2.3.5

Merge pull request #68 from friendsofstrandseq/weber8thomas/clean-con…

2.3.4

Bug Fixes

• common: Fix missing publishdir fct in common.smk #65 (Thomas Weber)

2.3.3

Bug Fixes

• slurm: Fix wrongly formated job time for slurm #62 (Thomas Weber)
• CI/CD: Fix GH actions #62 (Thomas Weber)
• CI/CD: Fix GH actions; update git submodules way to update #62 (Thomas Weber)
• CI/CD: Fix GH actions; update git submodules way to update ; remove needs section #62 (Thomas Weber)

Chores

• scripting: Add script to reorganise landsdorp data #62 (Thomas Weber)
• version: Upgrade to 2.3.4 #62 (Thomas Weber)

2.3.2

Full Changelog: 2.3.1...2.3.2

2.3.1

Commits

• 2c14ae0: Update Dockerfile-2.3.1.dockerfile (Thomas Weber)
• 47aa814: Bump mathieudutour/github-tag-action from 6.1 to 6.2 (dependabot[bot]) #58
• e833e70: Bump actions/checkout from 3.2.0 to 4.1.7 (dependabot[bot]) #60

2.2.5

• 7aab67b: Linting, fmt, config update (Thomas Weber) #56
• bae34f8: Small fix (Thomas Weber) #56
• 139bb5f: Small fix (Thomas Weber) #56
• 6253db5: Update dockerfile (Thomas Weber) #56
• 15b554f: Minor fixes for scNOVA (2.2.4) (Thomas Weber) #56
• 544673b: Dockerfile (Thomas Weber) #56
• 7d5db5e: Watchdog update, jbrowse mode (Thomas Weber) #56
• d68c375: Watchdog update, workshop progress, blacklisting fix, http remote provider change, more assertions, list_commands coloring fix (Thomas Weber) #56
• 389c63a: Watchdog update, workshop progress, blacklisting fix, http remote provider change, more assertions, list_commands coloring fix (Thomas Weber) #56
• 6804601: Watchdog update, workshop progress, blacklisting fix, http remote provider change, more assertions, list_commands coloring fix (Thomas Weber) #56
• 2d601f4: Watchdog update, workshop progress, blacklisting fix, http remote provider change, more assertions, list_commands coloring fix (Thomas Weber) #56
• cf054e0: Watchdog update, workshop progress, blacklisting fix, http remote provider change, more assertions, list_commands coloring fix (Thomas Weber) #56
• 99c2af4: Watchdog update, workshop progress, blacklisting fix, http remote provider change, more assertions, list_commands coloring fix (Thomas Weber) #56
• b7d0fab: Watchdog update, workshop progress, blacklisting fix, http remote provider change, more assertions, list_commands coloring fix (Thomas Weber) #56
• 1e36f1e: Stay on snakemake 7 (Thomas Weber) #56
• 72d1587: 2.2.5 (Thomas Weber) #56
• a942133: 2.2.5 with Dockerfile (Thomas Weber) #56
• dc49a21: Removing workflow/data & .tests (Thomas Weber) #56
• 48ad9f2: Removing workflow/data & .tests (Thomas Weber)
• b67a495: Remove .gitattributes to clear LFS tracking (Thomas Weber) #56
• 2b39288: Remove .gitattributes to clear LFS tracking (Thomas Weber)
• 5f3ebf6: Add submodules (Thomas Weber) #56
• 360282c: Add submodules (Thomas Weber)
• a952296: Updating GH actions, small fixes for v8 upgrade (Thomas Weber) #56
• 196e66f: Update GH actions (Thomas Weber) #56
• bac632e: Update GH actions (Thomas Weber) #56
• 74ef4a9: Update GH actions (Thomas Weber) #56
• 586651d: Updating GH actions, small fixes for v8 upgrade (Thomas Weber) #56
• 2d09737: Updating GH actions, small fixes for v8 upgrade (Thomas Weber) #56
• 9e32b48: Updating GH actions, small fixes for v8 upgrade (Thomas Weber) #56
• 7e8ac18: Updating GH actions, small fixes for v8 upgrade (Thomas Weber) #56
• 1844da8: Cleaning docs & updating GH actions (Thomas Weber) #56
• 280e638: Add dockerfile, minor fixes (Thomas Weber) #56
• 6005072: Fix image missing (Thomas Weber) #56
• 4d2e843: Merge (Thomas Weber) #56
• a25a714: Merge (Thomas Weber) #56

2.2.4

What's Changed

• 2.2.4: minor fixes for scNOVA new container mode by @weber8thomas in #51

Full Changelog: 2.2.2...2.2.4

2.2.2

What's Changed

• 2.2.2: IGV genome browsing & fixes by @weber8thomas in #50

Full Changelog: 2.2.1...2.2.2

2.2.1

Bug fixes

• Container fix
• Email fix

Full Changelog: 2.2.0...2.2.1

2.2.0

New parameters:

• ashleys_pipeline_only: target ashleys_pipeline output files to do manual selection afterwards ; liimit to the use of mosaicatcher-pipeline repo exclusively
• blacklist_regions: enable/disable blacklisting of regions

Bug fixes

• filter_bad_cells update and fix
• BAM SM tag check (counts.smk)
• fix of ms norm in mosaicatcher without using ashleys module
• scNOVA fix (slurm related)
• arbigent: create_hdf.py fix
• Fixing small indexing errors in plot-sv-calls_dev by @p-smirnov in #41

New Contributors

• @p-smirnov made their first contribution in #41

Full Changelog: 2.1.3...2.2.0