fix: qc report count typo fix #174
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* 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]>
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removing false section