chore: bump linting #232
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chore: bump linting #232
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visze
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Jan 7, 2026
* chore(master): release 0.5.4 * update plasmid example * update dockefile * fix: removed hard-coded barcode length (20) in hybrid reads (assignment workflow) (#213) * fix: hard-coded barcode length of 20 when using hybid FW read * fix: type error in stats * update github actions --------- Co-authored-by: Max Schubach <max.schubach@bihealth.de> * chore(master): release 0.5.5 (#214) Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * chore: add our recent preprint * assignment workflow: allow single end reads (FW only) (#218) * feat: allow single end reads * fix on qc report * documentation using MPRAsnakeflow without REV * Update workflow/rules/assignment/common.smk Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * code suggestions --------- Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * feat: bwa additional filtering (#216) * bwa-additional-filtering option added with their parameters * comment char results in errors when '#' in headers of the design file fixed by not using the comment function of read table * whitespace * Merge branch 'dev/additional_alignment_filtering' into master * snakefmt * snake case * fix linting * fix schema * magic * adding comments;added code used for 8k and 80k * trying to fix unnknown expected_length_filter * casting * casting functions * refactor * class * test * wirrdo * format * update expected_alignment_length * update doc * correct rule assignment_mapping_bwa_getBCs * spacces around infix operators * Update workflow/scripts/assignment/filter_bc_from_bam.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update workflow/scripts/assignment/filter_bc_from_bam.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update docs/1_getting_started/config.rst Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --------- Co-authored-by: Kilian Salomon <kilian.salomon@bih-charite.de> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * chore(master): release 0.5.6 (#219) * chore(master): release 0.5.6 * Update CHANGELOG with new features * Update Dockerfile version to 0.5.6 --------- Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Max <visze@users.noreply.github.com> * fix: max 255 read length allowed (#224) close #205 * chore(master): release 0.5.7 (#225) Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * fix: workaround for default values in schema files when using remote exec (#228) Too keep compatibility I set now the ExecMode to DEFAULT when it is REMOTE but only for the validation of the file. Afterwards I change it back. * fix: fixed various small bugs in mapping_bbmap.smk, attachBCToFastQ.py, quality_metrics.py (#220) * Fixed various small bugs * Update workflow/scripts/quality_metrics.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * revert commit Usually this is handled via the json schema and I do not want to introduce a second place with a default value. But unfortunately snakemake changed the way how it loads the defaults in json schema and does not use the default anymore.... --------- Co-authored-by: Grace Oualline <go274@r814u03n09.mccleary.ycrc.yale.edu> Co-authored-by: Max <visze@users.noreply.github.com> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * fix: issues in assignment check (#230) - Enhanced illegal character validation using regex pattern matching instead of simple bracket checking (#217) - Added case normalization (.upper()) for sequences and attached sequences (#221) - Fixed variable naming inconsistency (antisense_collition → antisense_collitions) closes #217 closes #221 * chore(master): release 0.5.8 (#229) Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * chore: bump linting (#232) * bump linting * fix: Adding Zenodo DOI to Readme (#231) * linting snakefmt 0.11.2 * readme update * update SPHINX documentation * chore(master): release 0.5.9 (#233) Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --------- Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Max Schubach <max.schubach@bihealth.de> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Co-authored-by: Kilian Salomon <kilian.salomon@bih-charite.de> Co-authored-by: g-walle <66499770+graceoualline@users.noreply.github.com> Co-authored-by: Grace Oualline <go274@r814u03n09.mccleary.ycrc.yale.edu>
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