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Dev 1.5.0 - #70

Merged

jfallmann merged 81 commits into

mainfrom

dev_1.5.0

Oct 15, 2026

Merged

Dev 1.5.0#70
jfallmann merged 81 commits into
mainfrom
dev_1.5.0

Commits on Jun 16, 2026
- added SPIT as DTU module
  jfallmann
  committed
  9a87176
Commits on Jun 23, 2026
- CI/CD push with Opus 4.8
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  c1a9dd4
- version config automation
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  54a007a
Commits on Jul 2, 2026
- added gene coordinates to all DE output to make it easier to catch CNV like patterns
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  a616bb0
Commits on Jul 3, 2026
- major overhaul of pseudomapping and single-cell processing. Moved to rust implementation of salmon, added rammap as minimap alternative, alevin-fry/piscem and simpleaf as well as oarfish. salmon ca…
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  c6e3953
Commits on Jul 4, 2026
- test coverage overhaul driven by Claude Fable, refactoring duplicated code into extra modules, removed dead code
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  2c1246c
- claude streamline of output paths between smk and nf where fixes where needed
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  38ac8b3
Commits on Jul 5, 2026
Commits on Jul 6, 2026
- Added Star-fusion in star or fastq mode, fable built tests and workflows based on CIRI2 template
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  da04552
Commits on Jul 7, 2026
- profile fixes and cleanup
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  7cd3db7
Commits on Jul 8, 2026
- fusion fix in header and tests
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  e04c81c
- fixed ctat ref detection, tests update, footer fix
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  f8c3f1d
- ctatlibdir detection fix
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  7ae5c70
- chr naming convention fix for fusion detection
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  f90339b
Commits on Jul 9, 2026
- fixed fusion paths
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  ecd4845
Commits on Jul 29, 2026
- added rustar as drop-in replacement for star with help from claude
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  0f37af3
Commits on Aug 11, 2026
- rammap env fix
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  f7d5cea
- added version constraint on containers, not all containers are built whenever a specific monsda version is released for exactly that version, keeps tooling clean and in direct line with conda envs
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  39deeff
Commits on Aug 12, 2026
- yamls updated, new container build started
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  e9b601a
Commits on Aug 13, 2026
- small fix for feature selection in counting without countreads
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  0db4d11
- rammap via conda env
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  cea1f23
Commits on Aug 14, 2026
- container dep fixes, added scripts for automization of build and push
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  a4b34ef
- container push fix
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  30238e5
- added rastqc as drop-in replacement for fastqc with gtpsol
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  97b83d2
- relaxed gz constraints to allow also bgz file endings
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  07b6958
Commits on Aug 17, 2026
Commits on Aug 18, 2026
Commits on Aug 19, 2026
- multiqc modules are case sensitive, fixed map from env to module
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  b001846
- build script path upadte
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  1c40b58
- typo
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  467004a
- set path via cli
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  75dc1db
- multiqc module and parameter fixes for all combinations of qc tools
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  bc0c949
- cleanup of multiqc params and output
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  625441a
- commiting agents.md
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  fb8c697
Commits on Aug 21, 2026
- troubleshoot section added to readme
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  f4f2285
Commits on Aug 24, 2026
- fixed multiqc input paths and tests for different run scenarios
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  adbb443
Commits on Aug 26, 2026
- added workaround for cases where umitools is invoked without extract
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  4c2f0c3
Commits on Aug 27, 2026
- shebang format
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  4c8d365
- hardened MDS plots for fewer samples, skipping if not enough instead of breaking
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  3f1063b
- single replicate fix for edger
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  4cbce3d
Commits on Aug 31, 2026
Commits on Sep 1, 2026
- fixed oarfish cli arguments for newer version
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  2f58130
- argument fixes for salmon
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  9cf744e
- added comprehensive test suite for cli arguments of all tools to check drifts for newer version
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  f51864d
- fixed versions for conda envs
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  f727525
Commits on Sep 2, 2026
- oarfish cannot handle gzipped gtf files currently fix
  jfallmann
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  d0fa734
Commits on Sep 18, 2026
- updated multiqc report with rastqc enabled and corresponding tests
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  2a6e359
Commits on Oct 5, 2026
- overhaul of DE logic before summary update
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  016cbcc
Commits on Oct 6, 2026
- Added new section PostDE to Analysis to automatically run GO/GSEA/GSVA analysis on selected cutoff output
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  3bd1f46
- more postDE wip
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  a81653d
- still postde WIP
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  e7e938b
- still wip
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  1cad1f7
- postde ready for testruns
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  8b8fb63
- ready to test on real data
  jfallmann
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  23d2731
- DE spike-in fixes
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  f36dc30
- proper spike-in size factor correction applied
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  7c2ba0e
- cleanup
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  6bb7db8
Commits on Oct 7, 2026
- Update to Readme
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  fe75c70
- spike-in normalization perpetuated to norm tables for tpm/cpm calculation properly
  jfallmann
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  223066c
Commits on Oct 8, 2026
Commits on Oct 9, 2026
- logging scaling factors for spike-normalized samples
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  95b462f
- profile updates for postde
  jfallmann
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  b77efff
- template fix
  jfallmann
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  619bd01
- added skill so claude and other agents can pick up monsda and know how to apply it
  jfallmann
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  17bd587
Commits on Oct 13, 2026
- fixed missing dependencies after cleanup for TRACKS
  jfallmann
  committed
  0bb9f91

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Commits on Oct 13, 2026