feat!: latest development for new release #133
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visze
commented
Nov 5, 2024
visze
commented
- outlier removal
- igvf outputs
- snakemake 8 required
- bbmap default mapq 30 and no min and max length within config
chore: update development to 0.1.0
* docs: enhancing documentation * docs: better quickstart * chore: ubdate github actions to setup-micromamba * docs: remove default channel from environment file * docs: improvements, like QC report (#125) * added .DS_Store to gitignore. * Fixed the overflow of the features section by using the table. * Fixed the broked report link. * fixed typo project * Typo fix controlled * Sample QC report HTML file * Added the link to the QC report in experiment. * Added the assignment QC report. * Add link to QC report in assignment documentation * Update documentation in quickstart.rst. Fixed typos and gramatical mistakes. * Update documentation in index.rst. Fix typos and grammatical mistakes. * Fix typo in installation documentation * Refactor documentation in config.rst --------- Co-authored-by: Max <visze@users.noreply.github.com> * docs: Fixed the link for the QC report in Experiment and Assignment (#126) * added .DS_Store to gitignore. * Fixed the overflow of the features section by using the table. * Fixed the broked report link. * fixed typo project * Typo fix controlled * Sample QC report HTML file * Added the link to the QC report in experiment. * Added the assignment QC report. * Add link to QC report in assignment documentation * Update documentation in quickstart.rst. Fixed typos and gramatical mistakes. * Update documentation in index.rst. Fix typos and grammatical mistakes. * Fix typo in installation documentation * Refactor documentation in config.rst * Update documentation links in assignment.rst and experiment.rst * Testing the iframe html file. * Update documentation links in assignment.rst and experiment.rst --------- Co-authored-by: Max <visze@users.noreply.github.com> * chore: delete not necessary files * docs: automatic versioning * style: automatic version printing of MPRAsnakeflow * fix: memory resources for bbmap (#123) * fix: add memory resources for bbmap * set lower memm in bbmap workflow profile * increasing memory for bmap --------- Co-authored-by: Max Schubach <max.schubach@bih-charite.de> Co-authored-by: Max Schubach <max.schubach@bihealth.de> * fix: Detach from anaconda (#122) * fix: detach from anaconda. Remove defaults conda channels * fixing linting errors * update hashes in dockerfile from lining errors --------- Co-authored-by: Max Schubach <max.schubach@bih-charite.de> * chore(master): release MPRAsnakeflow 0.1.1 (#124) * chore(master): release MPRAsnakeflow 0.1.1 * Update .release-please-manifest.json * Update version.txt * Update CHANGELOG.md --------- Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Max <visze@users.noreply.github.com> * forgot to upgrade two envs * docs: correct link in docs badge --------- Co-authored-by: Max Schubach <max.schubach@bih-charite.de> Co-authored-by: Ali <69039717+bioinformaticsguy@users.noreply.github.com> Co-authored-by: Max Schubach <max.schubach@bihealth.de> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
* refactor: removed statistics from final barcode to oligo map * refactor outputs * fix scripts due to renaming headers * fix assignment statistic due to new output * refactor!: moving files. not attched counts are not used as well as median for scaling * adding logs --------- Co-authored-by: Max Schubach <max.schubach@bih-charite.de>
Co-authored-by: Max Schubach <max.schubach@bih-charite.de>
Changes for bbmap * no min an max for sequence length and start. (like exact matching) * using default of 30 mapq instead of 35
* feat!: outlier detection Might break older config files * docs: update documentation for bbmap, apptainer and outlier removal * use abs for zscore * trying to fix outlier via zscore * mad code change * change outlier removal default to zscore --------- Co-authored-by: Max Schubach <max.schubach@bih-charite.de>
This was referenced Nov 5, 2024
This was referenced Nov 20, 2024
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