chore: development to newest version (#182)

* work * fix: experiment countplots (#149) Co-authored-by: Max Schubach <[email protected]> * chore(master): release MPRAsnakeflow 0.3.1 (#143) * chore(master): release MPRAsnakeflow 0.4.0 * Update .release-please-manifest.json * Update CHANGELOG.md * Update version.txt --------- Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Max <[email protected]> * chore: prepare for v0.4.0 (#154) * chore: Update development (#128) * 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 <[email protected]> * 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 <[email protected]> * 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 <[email protected]> Co-authored-by: Max Schubach <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * forgot to upgrade two envs * docs: correct link in docs badge --------- Co-authored-by: Max Schubach <[email protected]> Co-authored-by: Ali <[email protected]> Co-authored-by: Max Schubach <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * feat!: igvf outputs (#129) * 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 <[email protected]> * chore!: supporting only snakemake >=8.24.1 (#130) Co-authored-by: Max Schubach <[email protected]> * refactor!: No min max length for bbmap. default mapq is 30. (#131) 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 removal (#132) * 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 <[email protected]> * edit config * Update conventional-prs.yml * chore: update development (#142) * chore: conventional commit action (#134) * chore: Update development (#128) * 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 <[email protected]> * 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 <[email protected]> * 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 <[email protected]> Co-authored-by: Max Schubach <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * forgot to upgrade two envs * docs: correct link in docs badge --------- Co-authored-by: Max Schubach <[email protected]> Co-authored-by: Ali <[email protected]> Co-authored-by: Max Schubach <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * feat!: igvf outputs (#129) * 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 <[email protected]> * chore!: supporting only snakemake >=8.24.1 (#130) Co-authored-by: Max Schubach <[email protected]> * refactor!: No min max length for bbmap. default mapq is 30. (#131) 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 removal (#132) * 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 <[email protected]> * edit config * Update conventional-prs.yml --------- Co-authored-by: Max Schubach <[email protected]> Co-authored-by: Ali <[email protected]> Co-authored-by: Max Schubach <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * Update Dockerfile * chore(master): release MPRAsnakeflow 0.2.0 (#135) * chore(master): release MPRAsnakeflow 0.2.0 * Update CHANGELOG.md --------- Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Max <[email protected]> * feat!: versioned config (#140) * no mad outlier detection, version controled config, global config removed * getting action linter to run * fix: update argument syntax for version retrieval in GitHub Actions workflow * fix: correct argument syntax for version retrieval in GitHub Actions workflow * fix: correct argument syntax for version retrieval in GitHub Actions workflow * fix: update argument syntax for version retrieval in GitHub Actions workflow * fix: add skip version check option in workflow configuration --------- Co-authored-by: Max Schubach <[email protected]> * chore(master): release MPRAsnakeflow 0.3.0 (#141) * chore(master): release MPRAsnakeflow 0.3.0 * Update CHANGELOG.md --------- Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Max <[email protected]> --------- Co-authored-by: Max Schubach <[email protected]> Co-authored-by: Ali <[email protected]> Co-authored-by: Max Schubach <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * feat: one dna or RNA count file across multiple replicates (#144) * feat: using one experiment across all replicates for DNA (or RNA) * snakemake format --------- Co-authored-by: Max Schubach <[email protected]> * fix: plot per bc counts correlation when replicates are more than 3 (#145) * fix: error on plot size when using more that 3 replicates * per inser count also affected --------- Co-authored-by: Max Schubach <[email protected]> * feat: add label file to count basic configuration (#147) * feat: strand sensitive option (#146) * allowing additional properties for config back compatibility * work * implementing strand_senssitive config with interplay in snakemake file --------- Co-authored-by: Max Schubach <[email protected]> Co-authored-by: Max Schubach <[email protected]> * docs: documentation update * docs: formatting * chore: get latest fix (#151) * fix: experiment countplots (#149) Co-authored-by: Max Schubach <[email protected]> * chore(master): release MPRAsnakeflow 0.3.1 (#143) * chore(master): release MPRAsnakeflow 0.4.0 * Update .release-please-manifest.json * Update CHANGELOG.md * Update version.txt --------- Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Max <[email protected]> --------- Co-authored-by: Max Schubach <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * feat: allowing only FW reads with a UMI (#152) --------- Co-authored-by: Max Schubach <[email protected]> * feat: add performance tweaks for resource optimization in workflow rules (#153) Co-authored-by: Max Schubach <[email protected]> * update release-please github actions --------- Co-authored-by: Max Schubach <[email protected]> Co-authored-by: Ali <[email protected]> Co-authored-by: Max Schubach <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * chore: modify release-please manifest * chore: prepare for v0.4.0 (#157) * chore: Update development (#128) * 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 <[email protected]> * 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 <[email protected]> * 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 <[email protected]> Co-authored-by: Max Schubach <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * forgot to upgrade two envs * docs: correct link in docs badge --------- Co-authored-by: Max Schubach <[email protected]> Co-authored-by: Ali <[email protected]> Co-authored-by: Max Schubach <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * feat!: igvf outputs (#129) * 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 <[email protected]> * chore!: supporting only snakemake >=8.24.1 (#130) Co-authored-by: Max Schubach <[email protected]> * refactor!: No min max length for bbmap. default mapq is 30. (#131) 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 removal (#132) * 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 <[email protected]> * edit config * Update conventional-prs.yml * chore: update development (#142) * chore: conventional commit action (#134) * chore: Update development (#128) * 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 <[email protected]> * 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 <[email protected]> * 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 <[email protected]> Co-authored-by: Max Schubach <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * forgot to upgrade two envs * docs: correct link in docs badge --------- Co-authored-by: Max Schubach <[email protected]> Co-authored-by: Ali <[email protected]> Co-authored-by: Max Schubach <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * feat!: igvf outputs (#129) * 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 <[email protected]> * chore!: supporting only snakemake >=8.24.1 (#130) Co-authored-by: Max Schubach <[email protected]> * refactor!: No min max length for bbmap. default mapq is 30. (#131) 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 removal (#132) * 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 <[email protected]> * edit config * Update conventional-prs.yml --------- Co-authored-by: Max Schubach <[email protected]> Co-authored-by: Ali <[email protected]> Co-authored-by: Max Schubach <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * Update Dockerfile * chore(master): release MPRAsnakeflow 0.2.0 (#135) * chore(master): release MPRAsnakeflow 0.2.0 * Update CHANGELOG.md --------- Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Max <[email protected]> * feat!: versioned config (#140) * no mad outlier detection, version controled config, global config removed * getting action linter to run * fix: update argument syntax for version retrieval in GitHub Actions workflow * fix: correct argument syntax for version retrieval in GitHub Actions workflow * fix: correct argument syntax for version retrieval in GitHub Actions workflow * fix: update argument syntax for version retrieval in GitHub Actions workflow * fix: add skip version check option in workflow configuration --------- Co-authored-by: Max Schubach <[email protected]> * chore(master): release MPRAsnakeflow 0.3.0 (#141) * chore(master): release MPRAsnakeflow 0.3.0 * Update CHANGELOG.md --------- Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Max <[email protected]> --------- Co-authored-by: Max Schubach <[email protected]> Co-authored-by: Ali <[email protected]> Co-authored-by: Max Schubach <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * feat: one dna or RNA count file across multiple replicates (#144) * feat: using one experiment across all replicates for DNA (or RNA) * snakemake format --------- Co-authored-by: Max Schubach <[email protected]> * fix: plot per bc counts correlation when replicates are more than 3 (#145) * fix: error on plot size when using more that 3 replicates * per inser count also affected --------- Co-authored-by: Max Schubach <[email protected]> * feat: add label file to count basic configuration (#147) * feat: strand sensitive option (#146) * allowing additional properties for config back compatibility * work * implementing strand_senssitive config with interplay in snakemake file --------- Co-authored-by: Max Schubach <[email protected]> Co-authored-by: Max Schubach <[email protected]> * docs: documentation update * docs: formatting * chore: get latest fix (#151) * fix: experiment countplots (#149) Co-authored-by: Max Schubach <[email protected]> * chore(master): release MPRAsnakeflow 0.3.1 (#143) * chore(master): release MPRAsnakeflow 0.4.0 * Update .release-please-manifest.json * Update CHANGELOG.md * Update version.txt --------- Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Max <[email protected]> --------- Co-authored-by: Max Schubach <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * feat: allowing only FW reads with a UMI (#152) --------- Co-authored-by: Max Schubach <[email protected]> * feat: add performance tweaks for resource optimization in workflow rules (#153) Co-authored-by: Max Schubach <[email protected]> * update release-please github actions * chore: master to development (#156) * fix: experiment countplots (#149) Co-authored-by: Max Schubach <[email protected]> * chore(master): release MPRAsnakeflow 0.3.1 (#143) * chore(master): release MPRAsnakeflow 0.4.0 * Update .release-please-manifest.json * Update CHANGELOG.md * Update version.txt --------- Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Max <[email protected]> * chore: prepare for v0.4.0 (#154) * chore: Update development (#128) * 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 <[email protected]> * 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 <[email protected]> * 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 <[email protected]> Co-authored-by: Max Schubach <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * forgot to upgrade two envs * docs: correct link in docs badge --------- Co-authored-by: Max Schubach <[email protected]> Co-authored-by: Ali <[email protected]> Co-authored-by: Max Schubach <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * feat!: igvf outputs (#129) * 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 <[email protected]> * chore!: supporting only snakemake >=8.24.1 (#130) Co-authored-by: Max Schubach <[email protected]> * refactor!: No min max length for bbmap. default mapq is 30. (#131) 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 removal (#132) * 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 <[email protected]> * edit config * Update conventional-prs.yml * chore: update development (#142) * chore: conventional commit action (#134) * chore: Update development (#128) * 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 <[email protected]> * 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 <[email protected]> * 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 <[email protected]> Co-authored-by: Max Schubach <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * forgot to upgrade two envs * docs: correct link in docs badge --------- Co-authored-by: Max Schubach <[email protected]> Co-authored-by: Ali <[email protected]> Co-authored-by: Max Schubach <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * feat!: igvf outputs (#129) * 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 <[email protected]> * chore!: supporting only snakemake >=8.24.1 (#130) Co-authored-by: Max Schubach <[email protected]> * refactor!: No min max length for bbmap. default mapq is 30. (#131) 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 removal (#132) * 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 <[email protected]> * edit config * Update conventional-prs.yml --------- Co-authored-by: Max Schubach <[email protected]> Co-authored-by: Ali <[email protected]> Co-authored-by: Max Schubach <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * Update Dockerfile * chore(master): release MPRAsnakeflow 0.2.0 (#135) * chore(master): release MPRAsnakeflow 0.2.0 * Update CHANGELOG.md --------- Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Max <[email protected]> * feat!: versioned config (#140) * no mad outlier detection, version controled config, global config removed * getting action linter to run * fix: update argument syntax for version retrieval in GitHub Actions workflow * fix: correct argument syntax for version retrieval in GitHub Actions workflow * fix: correct argument syntax for version retrieval in GitHub Actions workflow * fix: update argument syntax for version retrieval in GitHub Actions workflow * fix: add skip version check option in workflow configuration --------- Co-authored-by: Max Schubach <[email protected]> * chore(master): release MPRAsnakeflow 0.3.0 (#141) * chore(master): release MPRAsnakeflow 0.3.0 * Update CHANGELOG.md --------- Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Max <[email protected]> --------- Co-authored-by: Max Schubach <[email protected]> Co-authored-by: Ali <[email protected]> Co-authored-by: Max Schubach <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * feat: one dna or RNA count file across multiple replicates (#144) * feat: using one experiment across all replicates for DNA (or RNA) * snakemake format --------- Co-authored-by: Max Schubach <[email protected]> * fix: plot per bc counts correlation when replicates are more than 3 (#145) * fix: error on plot size when using more that 3 replicates * per inser count also affected --------- Co-authored-by: Max Schubach <[email protected]> * feat: add label file to count basic configuration (#147) * feat: strand sensitive option (#146) * allowing additional properties for config back compatibility * work * implementing strand_senssitive config with interplay in snakemake file --------- Co-authored-by: Max Schubach <[email protected]> Co-authored-by: Max Schubach <[email protected]> * docs: documentation update * docs: formatting * chore: get latest fix (#151) * fix: experiment countplots (#149) Co-authored-by: Max Schubach <[email protected]> * chore(master): release MPRAsnakeflow 0.3.1 (#143) * chore(master): release MPRAsnakeflow 0.4.0 * Update .release-please-manifest.json * Update CHANGELOG.md * Update version.txt --------- Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Max <[email protected]> --------- Co-authored-by: Max Schubach <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * feat: allowing only FW reads with a UMI (#152) --------- Co-authored-by: Max Schubach <[email protected]> * feat: add performance tweaks for resource optimization in workflow rules (#153) Co-authored-by: Max Schubach <[email protected]> * update release-please github actions --------- Co-authored-by: Max Schubach <[email protected]> Co-authored-by: Ali <[email protected]> Co-authored-by: Max Schubach <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * chore: modify release-please manifest --------- Co-authored-by: Max Schubach <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Ali <[email protected]> Co-authored-by: Max Schubach <[email protected]> --------- Co-authored-by: Max Schubach <[email protected]> Co-authored-by: Ali <[email protected]> Co-authored-by: Max Schubach <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * chore: remove files (#158) Co-authored-by: Max Schubach <[email protected]> * feat: update license * feat!: version change because of config changes * chore(master): release 0.4.0 (#159) * chore(master): release 0.4.0 * Update CHANGELOG.md --------- Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Max <[email protected]> * fix: update configs to 0.4 * chore(master): release 0.4.1 * fix: swapped barcode output files * chore(master): release 0.4.2 * chore: Snakemake workflow catalog (#165) * Create README.md create README.md necessary to appear in standardized usage area of snakemake workflow catalog * Update README.md added caption * Create .snakemake-workflow-catalog.yaml file necessary for inclusion in standardized usage area in snakemake workflow catalog * Rename .snakemake-workflow-catalog.yaml to .snakemake-workflow-catalog.yml fix file name * Update .snakemake-workflow-catalog.yml fixed format errors * Update README.md addition of link to documentation and config file documentation * chore: adding default example config file for default and automatic linting * fix: swap activity threshold and all output file paths in qc_report rule (#172) Co-authored-by: Max Schubach <[email protected]> * chore(master): release 0.4.3 (#173) Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * fix: qc report count typo fix (#174) * chore(master): release 0.4.4 (#175) Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * changed the length of the sequence we want to check in the attach_sequence case (#177) Co-authored-by: Kilian Salomon <[email protected]> * fix: change the length of the sequence we want to check in the attach_sequence case (#177) Co-authored-by: Kilian Salomon <[email protected]> * chore(master): release 0.4.5 * Update CHANGELOG.md * refactor: code style * fix: revert v0.4.5. The fix was already implemented within the common.smk file * chore(master): release 0.4.6 --------- Co-authored-by: Max Schubach <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Ali <[email protected]> Co-authored-by: Nikola de Lange <[email protected]> Co-authored-by: Kilian <[email protected]> Co-authored-by: Kilian Salomon <[email protected]>
kircherlab · Feb 27, 2025 · 755f8e0 · 755f8e0
1 parent 153aaca
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diff --git a/.editorconfig b/.editorconfig
@@ -9,6 +9,7 @@ insert_final_newline = true
 charset = utf-8
 indent_style = space
 indent_size = 4
+max_line_length = 127
 
 [*.{yml,yaml}]
 indent_style = space
@@ -17,4 +18,3 @@ indent_size = 2
 [*.R]
 indent_style = space
 indent_size = 2
-max_line_length = 127
diff --git a/.release-please-manifest.json b/.release-please-manifest.json
@@ -1,3 +1,3 @@
 {
-  ".": "0.3.1"
+  ".": "0.4.6"
 }
diff --git a/.snakemake-workflow-catalog.yml b/.snakemake-workflow-catalog.yml
@@ -0,0 +1,6 @@
+---
+usage:
+  software-stack-deployment:
+    conda: true
+    singularity+conda: true
+  report: true
diff --git a/.vscode/settings.json b/.vscode/settings.json
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,13 +1,68 @@
 # Changelog
 
-## [0.3.1](https://github.com/kircherlab/MPRAsnakeflow/compare/MPRAsnakeflow-v0.3.0...MPRAsnakeflow-v0.3.1) (2024-12-17)
+## [0.4.6](https://github.com/kircherlab/MPRAsnakeflow/compare/v0.4.5...v0.4.6) (2025-02-26)
 
 
+### Bug Fixes
+
+* revert v0.4.5. The fix was already implemented within the common.smk file ([7997440](https://github.com/kircherlab/MPRAsnakeflow/commit/799744050b540d96545ac72bc2280e8e37a2b61e))
+
+## [0.4.5](https://github.com/kircherlab/MPRAsnakeflow/compare/v0.4.4...v0.4.5) (2025-02-24)
+
+
+### Bug Fixes
+
+* change the length of the sequence we want to check in the attach_sequence case ([#177](https://github.com/kircherlab/MPRAsnakeflow/issues/177)) ([e3db5cf](https://github.com/kircherlab/MPRAsnakeflow/commit/e3db5cf487423126ada0fda5305f42a0b38f25cb))
+
+## [0.4.4](https://github.com/kircherlab/MPRAsnakeflow/compare/v0.4.3...v0.4.4) (2025-02-05)
+
+
+### Bug Fixes
+
+* qc report count typo fix ([#174](https://github.com/kircherlab/MPRAsnakeflow/issues/174)) ([d78d339](https://github.com/kircherlab/MPRAsnakeflow/commit/d78d3391700c092c90742d1e47dc7b65b4d6d808))
+
+## [0.4.3](https://github.com/kircherlab/MPRAsnakeflow/compare/v0.4.2...v0.4.3) (2025-01-29)
+
+
+### Bug Fixes
+
+* swap activity threshold and all output file paths in qc_report rule ([#172](https://github.com/kircherlab/MPRAsnakeflow/issues/172)) ([ff1b11c](https://github.com/kircherlab/MPRAsnakeflow/commit/ff1b11cc3baf84a0a0c45201d93b36d8f630d42b))
+
+## [0.4.2](https://github.com/kircherlab/MPRAsnakeflow/compare/v0.4.1...v0.4.2) (2025-01-07)
+
+
+### Bug Fixes
+
+* swapped barcode output files ([a851ad2](https://github.com/kircherlab/MPRAsnakeflow/commit/a851ad2d74aad0834b853eb7432da10f369f8e21))
+
+## [0.4.1](https://github.com/kircherlab/MPRAsnakeflow/compare/v0.4.0...v0.4.1) (2025-01-06)
+
+
+### Bug Fixes
+
+* update configs to 0.4 ([bd79b6b](https://github.com/kircherlab/MPRAsnakeflow/commit/bd79b6b22118749a5eec89ec95815b243318dd25))
+
+## [0.4.0](https://github.com/kircherlab/MPRAsnakeflow/compare/v0.3.1...v0.4.0) (2025-01-02)
+
+
+### ⚠ BREAKING CHANGES
+
+* Major version change because of changes in config that are not backward compatible.
+
+### Features
+
+* Add performance tweaks for resource optimization in workflow rules ([5ed1ef9](https://github.com/kircherlab/MPRAsnakeflow/commit/5ed1ef9fb92acc56c999f26183e5ef0d4caf5be0))
+* Allowing also only FW reads with a UMI ([56b2254](https://github.com/kircherlab/MPRAsnakeflow/commit/56b225405bba024779edba11a332872b01ac02de))
+* Strand sensitive option ([f315aab](https://github.com/kircherlab/MPRAsnakeflow/commit/f315aabd24ebe6f524b9fb3b008f5af96987775d))
+* One DNA or RNA count file across multiple replicates ([ccbacee](https://github.com/kircherlab/MPRAsnakeflow/commit/ccbacee28bd551f9508e80d4e966188f970ba077))
+
+## [0.3.1](https://github.com/kircherlab/MPRAsnakeflow/compare/v0.3.0...v0.3.1) (2024-12-17)
+
 ### Bug Fixes
 
 * Wrong experiment count plots in QC report ([#149](https://github.com/kircherlab/MPRAsnakeflow/issues/149)) ([d2be468](https://github.com/kircherlab/MPRAsnakeflow/commit/d2be46891650ff9aaab61f750a4b3bc3b65e3e88))
 
-## [0.3.0](https://github.com/kircherlab/MPRAsnakeflow/compare/MPRAsnakeflow-v0.2.0...MPRAsnakeflow-v0.3.0) (2024-11-20)
+## [0.3.0](https://github.com/kircherlab/MPRAsnakeflow/compare/v0.2.0...v0.3.0) (2024-11-20)
 
 
 ### ⚠ BREAKING CHANGES
@@ -21,7 +76,7 @@
 * default is NO outlier detection (none is not present anymore) ([#140](https://github.com/kircherlab/MPRAsnakeflow/issues/140))
 * global config is removed. splits moved now withing mapping in assignment ([#140](https://github.com/kircherlab/MPRAsnakeflow/issues/140))
 
-## [0.2.0](https://github.com/kircherlab/MPRAsnakeflow/compare/MPRAsnakeflow-v0.1.1...MPRAsnakeflow-v0.2.0) (2024-11-05)
+## [0.2.0](https://github.com/kircherlab/MPRAsnakeflow/compare/v0.1.1...v0.2.0) (2024-11-05)
 
 ### ⚠ BREAKING CHANGES
 
@@ -39,14 +94,14 @@
 
 ### Bug Fixes
 
-## [0.1.1](https://github.com/kircherlab/MPRAsnakeflow/compare/MPRAsnakeflow-v0.1.0...MPRAsnakeflow-v0.1.1) (2024-09-30)
+## [0.1.1](https://github.com/kircherlab/MPRAsnakeflow/compare/v0.1.0...v0.1.1) (2024-09-30)
 
 ### Bug Fixes
 
 * Detach from anaconda ([#122](https://github.com/kircherlab/MPRAsnakeflow/issues/122)) ([16bcea2](https://github.com/kircherlab/MPRAsnakeflow/commit/16bcea2f04190a5965ad1865cf30f6dd44f1b6a0))
 * memory resources for bbmap ([#123](https://github.com/kircherlab/MPRAsnakeflow/issues/123)) ([af93f58](https://github.com/kircherlab/MPRAsnakeflow/commit/af93f588e9387ddf91197f5587d36c3481499b38))
 
-## [0.1.0](https://github.com/kircherlab/MPRAsnakeflow/compare/MPRAsnakeflow-v0.0.1...MPRAsnakeflow-v0.1.0) (2024-09-18)
+## [0.1.0](https://github.com/kircherlab/MPRAsnakeflow/compare/v0.0.1...v0.1.0) (2024-09-18)
 
 First release of MPRAsnakeflow! 
 

diff --git a/LICENSE b/LICENSE
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2021, Max Schubach, Berlin Institute of Health (BIH)
+Copyright (c) 2021, Max Schubach, Berlin Institute of Health at Charite - Universitatsmedizin Berlin
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/README.md b/README.md
@@ -117,7 +117,3 @@ In case you have also changed or added steps, please consider contributing them
 4. Commit and push your changes to your fork.
 5. Create a [pull request](https://help.github.com/en/articles/creating-a-pull-request) against the original repository.
 
-## Testing
-
-Test cases are in the subfolder `.test`. They are automatically executed via continuous integration with [Github Actions](https://github.com/features/actions).
-
diff --git a/config/README.md b/config/README.md
@@ -0,0 +1,4 @@
+## General configurations
+Create or adjust the `config/example_config.yaml` in the repository to your needs to configure the workflow execution. When running on a cluster environment you need a special [executor plugin](https://snakemake.github.io/snakemake-plugin-catalog/), e.g. like [SLURM](https://snakemake.github.io/snakemake-plugin-catalog/plugins/executor/slurm.html), and use an adapted workflow profile (original `profiles/default/config.yaml`) to set the correct values (like slurm partitions).
+
+Detailed information about the config file can be found in the [MPRAsnakeflow documentation](https://mprasnakeflow.readthedocs.io/latest/index.html) under [Config file](https://mprasnakeflow.readthedocs.io/latest/config.html).
diff --git a/config/example_assignment_bbmap.yaml b/config/example_assignment_bbmap.yaml
@@ -1,5 +1,5 @@
 ---
-version: "0.3"
+version: "0.4"
 assignments:
   exampleAssignment: # name of an example assignment (can be any string)
     bc_length: 15

diff --git a/config/example_assignment_bwa.yaml b/config/example_assignment_bwa.yaml
@@ -1,5 +1,5 @@
 ---
-version: "0.3"
+version: "0.4"
 assignments:
   exampleAssignment: # name of an example assignment (can be any string)
     bc_length: 15

diff --git a/config/example_assignment_exact_lazy.yaml b/config/example_assignment_exact_lazy.yaml
@@ -1,5 +1,5 @@
 ---
-version: "0.3"
+version: "0.4"
 assignments:
   exampleAssignment: # name of an example assignment (can be any string)
     bc_length: 15

diff --git a/config/example_assignment_exact_linker.yaml b/config/example_assignment_exact_linker.yaml
@@ -1,5 +1,5 @@
 ---
-version: "0.3"
+version: "0.4"
 assignments:
   exampleAssignment: # name of an example assignment (can be any string)
     bc_length: 20

diff --git a/config/example_config.yaml b/config/example_config.yaml
@@ -1,5 +1,5 @@
 ---
-version: "0.3"
+version: "0.4"
 assignments:
   exampleAssignment: # name of an example assignment (can be any string)
     bc_length: 15

diff --git a/config/example_count.yaml b/config/example_count.yaml
@@ -1,5 +1,5 @@
 ---
-version: "0.3"
+version: "0.4"
 experiments:
   exampleCount:
     bc_length: 15

diff --git a/profiles/default/config.yaml b/profiles/default/config.yaml
@@ -1,4 +1,5 @@
 ---
+configfile: config/example_config.yaml
 software-deployment-method: conda
 default-resources:
   slurm_partition: debug
@@ -42,7 +43,7 @@ set-resources:
     mem: 10G
     slurm_partition: medium
   assignment_mapping_bbmap:
-    runtime: 120
+    runtime: 240
     mem: 10G
     slurm_partition: medium
   assignment_collect:

diff --git a/resources/assoc_basic/config.yml b/resources/assoc_basic/config.yml
@@ -1,5 +1,5 @@
 ---
-version: "0.3"
+version: "0.4"
 assignments:
   assocBasic:
     bc_length: 15

diff --git a/resources/combined_basic/config.yml b/resources/combined_basic/config.yml
@@ -1,5 +1,5 @@
 ---
-version: "0.3"
+version: "0.4"
 assignments:
   assocBasic:
     bc_length: 15

diff --git a/resources/count_basic/config.yml b/resources/count_basic/config.yml
@@ -1,5 +1,5 @@
 ---
-version: "0.3"
+version: "0.4"
 experiments:
   exampleCount:
     bc_length: 15

diff --git a/version.txt b/version.txt
@@ -1 +1 @@
-0.3.1
+0.4.6
diff --git a/workflow/rules/qc_report.smk b/workflow/rules/qc_report.smk
@@ -86,8 +86,8 @@ rule qc_report_count:
         counts_per_oligo="results/experiments/{project}/statistic/assigned_counts/{assignment}/{config}/{condition}_barcodesPerInsert.png",
         counts_per_bc_dna="results/experiments/{project}/statistic/barcode/assigned_counts/{assignment}/{condition}_{config}_DNA_perBarcode.png",
         counts_per_bc_rna="results/experiments/{project}/statistic/barcode/assigned_counts/{assignment}/{condition}_{config}_RNA_perBarcode.png",
-        activity_thresh="results/experiments/{project}/statistic/assigned_counts/{assignment}/{config}/{condition}_group_barcodesPerInsert_box.png",
-        activity_all="results/experiments/{project}/statistic/assigned_counts/{assignment}/{config}/{condition}_group_barcodesPerInsert_box_minThreshold.png",
+        activity_all="results/experiments/{project}/statistic/assigned_counts/{assignment}/{config}/{condition}_group_barcodesPerInsert_box.png",
+        activity_thresh="results/experiments/{project}/statistic/assigned_counts/{assignment}/{config}/{condition}_group_barcodesPerInsert_box_minThreshold.png",
         dna_over_rna="results/experiments/{project}/statistic/assigned_counts/{assignment}/{config}/{condition}_dna_vs_rna.png",
         dna_over_rna_thresh="results/experiments/{project}/statistic/assigned_counts/{assignment}/{config}/{condition}_dna_vs_rna_minThreshold.png",
     output:

diff --git a/workflow/scripts/assignment/check_design_file.py b/workflow/scripts/assignment/check_design_file.py
@@ -42,18 +42,18 @@
     help="Using a simple dictionary to find identical sequences. This is faster but uses only the whole (or center part depending on start/length) of the design file. But in theory a substring can only be present and for more correct, but slower, search use the --slow-string-search.",
 )
 @click.option(
-    '--sequence-check', 
-    'sequence_check', 
-    type=click.Choice(['skip', 'sense_only', 'sense_antisense']), 
-    default='sense_antisense', 
-    help='Choose the type of sequence check. When set to skip, the script will not check for sequence collisions. This is useful when you know collisions but still want to preoceed with the design file.'
+    "--sequence-check",
+    "sequence_check",
+    type=click.Choice(["skip", "sense_only", "sense_antisense"]),
+    default="sense_antisense",
+    help="Choose the type of sequence check. When set to skip, the script will not check for sequence collisions. This is useful when you know collisions but still want to preoceed with the design file.",
 )
 @click.option(
     "--attach-sequence",
     "attach_sequence",
     required=False,
     type=(click.STRING, click.STRING),
-    help="Attach a sequence left and right to each entry of the fasta file."
+    help="Attach a sequence left and right to each entry of the fasta file.",
 )
 @click.option(
     "--output",
@@ -70,14 +70,13 @@ def cli(input_file, start, length, fast_search, sequence_check, attach_sequence,
     antisense_collitions = []
 
     # attach sequence
-    with open(output, 'w') as fasta_file:
+    with open(output, "w") as fasta_file:
         for name, seq in pyfastx.Fasta(input_file, build_index=False):
             new_sequence = seq
             if attach_sequence:
                 new_sequence = attach_sequence[0] + new_sequence + attach_sequence[1]
             fasta_file.write(f">{name}\n{new_sequence}\n")
 
-
     # read fasta file
     fa = pyfastx.Fasta(output)
 
@@ -90,22 +89,19 @@ def cli(input_file, start, length, fast_search, sequence_check, attach_sequence,
 
     # check for illegal characters
     click.echo("Searching for illegal characters in header...")
-    illegal_characters = np.array(
-        [True if "[" in i or "]" in i else False for i in set(ids)], dtype=bool
-    ).sum()
+    illegal_characters = np.array([True if "[" in i or "]" in i else False for i in set(ids)], dtype=bool).sum()
     if illegal_characters > 0:
         click.echo(
             f"{illegal_characters} headers contain illegal characters ('[',']').",
             err=True,
         )
         exit(1)
 
-
     # read fasta file
     if attach_sequence:
         fa = pyfastx.Fasta(output)
 
-    if sequence_check != 'skip':
+    if sequence_check != "skip":
         # build seq dict
         click.echo("Building sequence dictionary...")
         for i in range(len(fa)):
@@ -129,12 +125,16 @@ def cli(input_file, start, length, fast_search, sequence_check, attach_sequence,
             antisense_collition = set()
             if fast_search:
                 forward_collition.update(seq_dict.get(sub_seq_forward, set()))
-                antisense_collition.update(seq_dict.get(sub_seq_antisense, set())) if sequence_check == 'sense_antisense' else None
+                (
+                    antisense_collition.update(seq_dict.get(sub_seq_antisense, set()))
+                    if sequence_check == "sense_antisense"
+                    else None
+                )
             else:
                 for seq, names in seq_dict.items():
                     if sub_seq_forward in seq:
                         forward_collition.update(names)
-                    if sequence_check == 'sense_antisense' and sub_seq_antisense in seq:
+                    if sequence_check == "sense_antisense" and sub_seq_antisense in seq:
                         antisense_collition.update(names)
 
             if len(forward_collition) > 1:
@@ -143,12 +143,8 @@ def cli(input_file, start, length, fast_search, sequence_check, attach_sequence,
                 antisense_collitions.append(antisense_collition)
 
         # unique names
-        forward_collitions = [
-            list(i) for i in set(tuple(i) for i in forward_collitions)
-        ]
-        antisense_collition = [
-            list(i) for i in set(tuple(i) for i in antisense_collition)
-        ]
+        forward_collitions = [list(i) for i in set(tuple(i) for i in forward_collitions)]
+        antisense_collition = [list(i) for i in set(tuple(i) for i in antisense_collition)]
 
         if (len(forward_collitions) > 0) or (len(antisense_collitions) > 0):
             click.echo(
@@ -164,7 +160,7 @@ def cli(input_file, start, length, fast_search, sequence_check, attach_sequence,
                     "\t".join(forward_collitions[i]),
                     err=True,
                 )
-            if sequence_check == 'sense_antisense':
+            if sequence_check == "sense_antisense":
                 click.echo(
                     "-----------------ANTISENSE COLLISIONS-----------------",
                     err=True,

diff --git a/workflow/scripts/count/merge_replicates_barcode_counts.py b/workflow/scripts/count/merge_replicates_barcode_counts.py
@@ -21,14 +21,14 @@
 )
 @click.option(
     "--output",
-    "output_threshold_file",
+    "output_file",
     required=True,
     type=click.Path(writable=True),
     help="Output file.",
 )
 @click.option(
     "--output-threshold",
-    "output_file",
+    "output_threshold_file",
     required=True,
     type=click.Path(writable=True),
     help="Output file.",

diff --git a/workflow/scripts/report/qc_report_count.qmd b/workflow/scripts/report/qc_report_count.qmd
@@ -227,10 +227,6 @@ df_single.style.hide(axis="index").format( precision=2)
 
 :::
 
-# Number of barcodes per oligo
-
- Median is red, mean is blue.
-
 
 # Histograms barcodes per oligo, counts per barcode
-Original file line number
+Diff line change
@@ Expand Up / @@ -227,10 +227,6 @@ df_single.style.hide(axis="index").format( precision=2) @@
     :::
-    # Number of barcodes per oligo
-     Median is red, mean is blue.
     # Histograms barcodes per oligo, counts per barcode
@@ Expand Down @@