chore: master to development (kircherlab#156)

* fix: experiment countplots (kircherlab#149)

Co-authored-by: Max Schubach <[email protected]>

* chore(master): release MPRAsnakeflow 0.3.1 (kircherlab#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 (kircherlab#154)

* chore: Update development (kircherlab#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 (kircherlab#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 (kircherlab#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 (kircherlab#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 (kircherlab#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 (kircherlab#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 (kircherlab#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 (kircherlab#130)

Co-authored-by: Max Schubach <[email protected]>

* refactor!: No min max length for bbmap. default mapq is 30. (kircherlab#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 (kircherlab#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 (kircherlab#142)

* chore: conventional commit action (kircherlab#134)

* chore: Update development (kircherlab#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 (kircherlab#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 (kircherlab#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 (kircherlab#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 (kircherlab#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 (kircherlab#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 (kircherlab#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 (kircherlab#130)

Co-authored-by: Max Schubach <[email protected]>

* refactor!: No min max length for bbmap. default mapq is 30. (kircherlab#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 (kircherlab#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 (kircherlab#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 (kircherlab#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 (kircherlab#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 (kircherlab#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 (kircherlab#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 (kircherlab#147)

* feat: strand sensitive option (kircherlab#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 (kircherlab#151)

* fix: experiment countplots (kircherlab#149)

Co-authored-by: Max Schubach <[email protected]>

* chore(master): release MPRAsnakeflow 0.3.1 (kircherlab#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 (kircherlab#152)




---------

Co-authored-by: Max Schubach <[email protected]>

* feat: add performance tweaks for resource optimization in workflow rules (kircherlab#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]>

.github/release-please-config.json

@@ -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
         }
     }
 }