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chore: prepare for v0.4.0 #157

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Jan 2, 2025
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e8d4007
Merge pull request #120 from kircherlab/master
visze Sep 19, 2024
e647309
chore: Update development (#128)
visze Oct 17, 2024
b112d9c
feat!: igvf outputs (#129)
visze Oct 28, 2024
2d80faf
chore!: supporting only snakemake >=8.24.1 (#130)
visze Oct 28, 2024
1e9157b
refactor!: No min max length for bbmap. default mapq is 30. (#131)
visze Oct 28, 2024
e08c38a
feat!: outlier removal (#132)
visze Nov 5, 2024
2cf2ccf
Merge branch 'master' into development
visze Nov 5, 2024
58c55c3
edit config
visze Nov 5, 2024
163ccdd
Update conventional-prs.yml
visze Nov 5, 2024
64e8d9f
Merge branch 'master' of https://github.com/kircherlab/MPRAsnakeflow …
visze Nov 5, 2024
02076d9
chore: update development (#142)
visze Nov 20, 2024
f1944b8
Merge branches 'development' and 'master' of https://github.com/kirch…
visze Dec 5, 2024
ccbacee
feat: one dna or RNA count file across multiple replicates (#144)
visze Dec 6, 2024
22ce4d7
fix: plot per bc counts correlation when replicates are more than 3 (…
visze Dec 9, 2024
3c91a6a
feat: add label file to count basic configuration (#147)
bioinformaticsguy Dec 9, 2024
f315aab
feat: strand sensitive option (#146)
visze Dec 9, 2024
fd40828
docs: documentation update
visze Dec 9, 2024
9dc0f6f
docs: formatting
visze Dec 9, 2024
e317560
chore: get latest fix (#151)
visze Dec 17, 2024
56b2254
feat: allowing only FW reads with a UMI (#152)
visze Dec 17, 2024
5ed1ef9
feat: add performance tweaks for resource optimization in workflow ru…
visze Dec 18, 2024
854d293
update release-please github actions
visze Jan 2, 2025
153aaca
chore: master to development (#156)
visze Jan 2, 2025
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chore: master to development (#156)
* fix: experiment countplots (#149)

Co-authored-by: Max Schubach <max.schubach@bih-charite.de>

* 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 <visze@users.noreply.github.com>

* 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 <visze@users.noreply.github.com>

* docs: Fixed the link for the QC report in Experiment and Assignment (#126)

* added .DS_Store to gitignore.

* Fixed the overflow of the features section by using the table.

* Fixed the broked report link.

* fixed typo project

* Typo fix controlled

* Sample QC report HTML file

* Added the link to the QC report in experiment.

* Added the assignment QC report.

* Add link to QC report in assignment documentation

* Update documentation in quickstart.rst. Fixed typos and gramatical mistakes.

* Update documentation in index.rst. Fix typos and grammatical mistakes.

* Fix typo in installation documentation

* Refactor documentation in config.rst

* Update documentation links in assignment.rst and experiment.rst

* Testing the iframe html file.

* Update documentation links in assignment.rst and experiment.rst

---------

Co-authored-by: Max <visze@users.noreply.github.com>

* chore: delete not necessary files

* docs: automatic versioning

* style: automatic version printing of MPRAsnakeflow

* fix: memory resources for bbmap (#123)

* fix: add memory resources for bbmap

* set lower memm in bbmap workflow profile

* increasing memory for bmap

---------

Co-authored-by: Max Schubach <max.schubach@bih-charite.de>
Co-authored-by: Max Schubach <max.schubach@bihealth.de>

* fix: Detach from anaconda (#122)

* fix: detach from anaconda. Remove defaults conda channels

* fixing linting errors

* update hashes in dockerfile from lining errors

---------

Co-authored-by: Max Schubach <max.schubach@bih-charite.de>

* chore(master): release MPRAsnakeflow 0.1.1 (#124)

* chore(master): release MPRAsnakeflow 0.1.1

* Update .release-please-manifest.json

* Update version.txt

* Update CHANGELOG.md

---------

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Max <visze@users.noreply.github.com>

* forgot to upgrade two envs

* docs: correct link in docs badge

---------

Co-authored-by: Max Schubach <max.schubach@bih-charite.de>
Co-authored-by: Ali <69039717+bioinformaticsguy@users.noreply.github.com>
Co-authored-by: Max Schubach <max.schubach@bihealth.de>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

* 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 <max.schubach@bih-charite.de>

* chore!: supporting only snakemake >=8.24.1 (#130)

Co-authored-by: Max Schubach <max.schubach@bih-charite.de>

* 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 <max.schubach@bih-charite.de>

* 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 <visze@users.noreply.github.com>

* docs: Fixed the link for the QC report in Experiment and Assignment (#126)

* added .DS_Store to gitignore.

* Fixed the overflow of the features section by using the table.

* Fixed the broked report link.

* fixed typo project

* Typo fix controlled

* Sample QC report HTML file

* Added the link to the QC report in experiment.

* Added the assignment QC report.

* Add link to QC report in assignment documentation

* Update documentation in quickstart.rst. Fixed typos and gramatical mistakes.

* Update documentation in index.rst. Fix typos and grammatical mistakes.

* Fix typo in installation documentation

* Refactor documentation in config.rst

* Update documentation links in assignment.rst and experiment.rst

* Testing the iframe html file.

* Update documentation links in assignment.rst and experiment.rst

---------

Co-authored-by: Max <visze@users.noreply.github.com>

* chore: delete not necessary files

* docs: automatic versioning

* style: automatic version printing of MPRAsnakeflow

* fix: memory resources for bbmap (#123)

* fix: add memory resources for bbmap

* set lower memm in bbmap workflow profile

* increasing memory for bmap

---------

Co-authored-by: Max Schubach <max.schubach@bih-charite.de>
Co-authored-by: Max Schubach <max.schubach@bihealth.de>

* fix: Detach from anaconda (#122)

* fix: detach from anaconda. Remove defaults conda channels

* fixing linting errors

* update hashes in dockerfile from lining errors

---------

Co-authored-by: Max Schubach <max.schubach@bih-charite.de>

* chore(master): release MPRAsnakeflow 0.1.1 (#124)

* chore(master): release MPRAsnakeflow 0.1.1

* Update .release-please-manifest.json

* Update version.txt

* Update CHANGELOG.md

---------

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Max <visze@users.noreply.github.com>

* forgot to upgrade two envs

* docs: correct link in docs badge

---------

Co-authored-by: Max Schubach <max.schubach@bih-charite.de>
Co-authored-by: Ali <69039717+bioinformaticsguy@users.noreply.github.com>
Co-authored-by: Max Schubach <max.schubach@bihealth.de>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

* 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 <max.schubach@bih-charite.de>

* chore!: supporting only snakemake >=8.24.1 (#130)

Co-authored-by: Max Schubach <max.schubach@bih-charite.de>

* 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 <max.schubach@bih-charite.de>

* edit config

* Update conventional-prs.yml

---------

Co-authored-by: Max Schubach <max.schubach@bih-charite.de>
Co-authored-by: Ali <69039717+bioinformaticsguy@users.noreply.github.com>
Co-authored-by: Max Schubach <max.schubach@bihealth.de>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

* 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 <visze@users.noreply.github.com>

* 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 <max.schubach@bih-charite.de>

* 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 <visze@users.noreply.github.com>

---------

Co-authored-by: Max Schubach <max.schubach@bih-charite.de>
Co-authored-by: Ali <69039717+bioinformaticsguy@users.noreply.github.com>
Co-authored-by: Max Schubach <max.schubach@bihealth.de>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

* 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 <max.schubach@bih-charite.de>

* 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 <max.schubach@bih-charite.de>

* 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 <max.schubach@bih-charite.de>
Co-authored-by: Max Schubach <max.schubach@bihealth.de>

* docs: documentation update

* docs: formatting

* chore: get latest fix (#151)

* fix: experiment countplots (#149)

Co-authored-by: Max Schubach <max.schubach@bih-charite.de>

* 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 <visze@users.noreply.github.com>

---------

Co-authored-by: Max Schubach <max.schubach@bih-charite.de>
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 <max.schubach@bih-charite.de>

* feat: add performance tweaks for resource optimization in workflow rules (#153)

Co-authored-by: Max Schubach <max.schubach@bih-charite.de>

* update release-please github actions

---------

Co-authored-by: Max Schubach <max.schubach@bih-charite.de>
Co-authored-by: Ali <69039717+bioinformaticsguy@users.noreply.github.com>
Co-authored-by: Max Schubach <max.schubach@bihealth.de>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

* chore: modify release-please manifest

---------

Co-authored-by: Max Schubach <max.schubach@bih-charite.de>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Ali <69039717+bioinformaticsguy@users.noreply.github.com>
Co-authored-by: Max Schubach <max.schubach@bihealth.de>
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5 people authored Jan 2, 2025
commit 153aaca7f8733acc1ecb9706ab490d0e01fe7eb4
3 changes: 2 additions & 1 deletion .github/release-please-config.json
Original file line number Diff line number Diff line change
@@ -10,7 +10,8 @@
"bump-patch-for-minor-pre-major": true,
"draft": false,
"prerelease": true,
"tag-prefix": "v"
"tag-prefix": "v",
"include-component-in-tag": false
}
}
}
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