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feat!: refactoring of workflow to make it more flexible, remove hardcoded options#32

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rabioinf merged 27 commits intomainfrom
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Mar 12, 2026
Merged

feat!: refactoring of workflow to make it more flexible, remove hardcoded options#32
rabioinf merged 27 commits intomainfrom
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@m-jahn m-jahn commented Oct 13, 2025

  • PR is a major refactoring of wf attempting to remove certain problems
  • removes the hardcoded options of three protocols and implements choice of correct methods via config file only
  • removed redundant rules for if-clauses on protocols as well as paired-/single-end methods
  • these are all replaced with decision logic inside rules
  • added schemas
  • added config README
  • replaced a range of tools with snakemake wrappers for easier maintenance
  • PR addresses a number of issues: closes replace common tools with wrappers #31 closes suggestion to circumvent hard-coded options #26 closes add sample sheet validation #6 closes add config file validation #7
  • PR is a braking change as the sample sheet layout has option experiment removed
  • wf was tested with all test data sets and 1 full dataset for the NEB UMI protcol and found to have almost identical results, also for DE using the DESeq workflow on top

m-jahn added 15 commits September 25, 2025 07:59
@m-jahn
fix: update catalog yaml
e5cfedb
@m-jahn
fix: simplified sample paths, removed unlisting
e147f05
@m-jahn
feat: split READMEs according to catalog standard
b5fdbe1
@m-jahn
fix: remove style config as it deviates from prettier standard
ea4a4ea
@m-jahn
fix: update GH actions wfs
e38c83f
@m-jahn
feat: major refactoring of logic and replacement of custom rules with…
f8b5da4 
… wrappers
@m-jahn
fix: replaced samtools flagstat with wrapper
83ebbf5
@m-jahn
fix: UMI extraction and dedup for all protocols
6b9376b
@m-jahn
fix: added fastp and simplified fastqc input for multiqc
d516912
@m-jahn
fix: update docs and removing redundancies
09d3fa5
@m-jahn
feat: added schemas, closes #6, closes #7
4be847d
@m-jahn
fix: update for config was missing
74ca2ca
@m-jahn
fix: linting on test dir
861e5fb
@m-jahn
fix: unified all thread defs, enable test run with sufficient threads
237e17b
@m-jahn
fix: add number of cores to report
fc38bea
@m-jahn m-jahn requested a review from rabioinf October 13, 2025 07:40
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github-actions Bot commented Mar 5, 2026

Super-linter summary

Language Validation result
SNAKEMAKE_SNAKEFMT Pass ✅
YAML_PRETTIER Pass ✅

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github-actions Bot commented Mar 6, 2026

Super-linter summary

Language Validation result
SNAKEMAKE_SNAKEFMT Pass ✅
YAML_PRETTIER Pass ✅

All files and directories linted successfully

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rabioinf
rabioinf approved these changes Mar 6, 2026
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looks good now.

@rabioinf rabioinf merged commit 4eec975 into main Mar 12, 2026
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replace common tools with wrappers suggestion to circumvent hard-coded options add config file validation add sample sheet validation

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@m-jahn @rabioinf