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>

.github/workflows/conventional-prs.yml

@@ -1,5 +1,5 @@
 ---
-name: PR
+name: "Lint PR"
 on:
   pull_request_target:
     types:
@@ -8,12 +8,14 @@ on:
       - edited
       - synchronize
 
+permissions:
+  pull-requests: read
+
 jobs:
-  title-format:
+  main:
+    name: Validate PR title
     runs-on: ubuntu-latest
     steps:
-      - uses: amannn/action-semantic-pull-request@v4
+      - uses: amannn/action-semantic-pull-request@v5
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        with:
-          validateSingleCommit: true