Merging Feat/selection

.editorconfig

@@ -8,8 +8,62 @@ trim_trailing_whitespace = true
 indent_size = 4
 indent_style = space
 
-[*.{md,yml,yaml,cff}]
+[*.{md,yml,yaml,html,css,scss,js,cff}]
 indent_size = 2
 
-[*.nf.test]
-insert_final_newline = false
+# These files are edited and tested upstream in nf-core/modules
+[/modules/nf-core/**]
+charset = unset
+end_of_line = unset
+insert_final_newline = unset
+trim_trailing_whitespace = unset
+indent_style = unset
+indent_size = unset
+
+[/subworkflows/nf-core/**]
+charset = unset
+end_of_line = unset
+insert_final_newline = unset
+trim_trailing_whitespace = unset
+indent_style = unset
+indent_size = unset
+
+# These files are edited and tested upstream in pfr/modules
+[/modules/pfr/**]
+charset = unset
+end_of_line = unset
+insert_final_newline = unset
+trim_trailing_whitespace = unset
+indent_style = unset
+indent_size = unset
+
+[/subworkflows/pfr/**]
+charset = unset
+end_of_line = unset
+insert_final_newline = unset
+trim_trailing_whitespace = unset
+indent_style = unset
+indent_size = unset
+
+[/assets/email*]
+indent_size = unset
+
+# ignore Readme
+[README.md]
+indent_style = unset
+
+# ignore python
+[*.{py}]
+indent_style = unset
+
+# ignore perl
+[*.{pl,pm}]
+indent_size = unset
+
+# ignore drawio
+[*.drawio]
+indent_size = unset
+
+# ignore LICENSE
+[LICENSE]
+indent_size = unset

.github/workflows/test.yml

@@ -13,37 +13,22 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-  prettier:
-    runs-on: ubuntu-latest
-    steps:
-      - name: Check out repository
-        uses: actions/checkout@v4
-
-      - name: Install NodeJS
-        uses: actions/setup-node@v4
-        with:
-          node-version: "20"
-
-      - name: Install Prettier
-        run: npm install -g prettier
-
-      - name: Run Prettier --check
-        run: prettier --check .
-
-  editorconfig:
+  pre-commit:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
 
-      - uses: actions/setup-node@v4
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
         with:
-          node-version: "20"
+          python-version: 3.11
+          cache: "pip"
 
-      - name: Install editorconfig-checker
-        run: npm install -g editorconfig-checker
+      - name: Install pre-commit
+        run: pip install pre-commit
 
-      - name: Run ECLint check
-        run: editorconfig-checker -exclude README.md $(git ls-files | grep -v test | grep -v LICENSE)
+      - name: Run pre-commit
+        run: pre-commit run --all-files
 
   stub-test:
     runs-on: ubuntu-latest
@@ -54,31 +39,22 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - uses: actions/checkout@v4
-        with:
-          repository: PlantandFoodResearch/pangene-test
-          ssh-key: ${{ secrets.PANGENE_TEST_DEPLOY_KEY }}
-          path: pangene-test
-
-      - uses: actions/setup-java@v3
-        with:
-          distribution: "temurin"
-          java-version: "17"
-      - name: Setup Nextflow
+      - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
+        with:
+          version: "23.04.4"
 
       - name: Run stub-test
         run: |
-          nextflow \
+          nextflow run \
             main.nf \
             -profile local,docker \
-            -resume \
             -stub \
-            -params-file conf/test_params.json
+            -params-file tests/stub/params.json
 
   confirm-pass:
     runs-on: ubuntu-latest
-    needs: [prettier, editorconfig, stub-test]
+    needs: [pre-commit, stub-test]
     if: always()
     steps:
       - name: All tests ok

.gitignore

@@ -12,5 +12,4 @@ __pycache__
 *.stdout
 *.stderr
 
-.literature
 pangene-test/

.pre-commit-config.yaml

@@ -3,3 +3,18 @@ repos:
     rev: "v3.1.0"
     hooks:
       - id: prettier
+  - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
+    rev: "2.7.3"
+    hooks:
+      - id: editorconfig-checker
+        alias: ec
+  - repo: local
+    hooks:
+      - id: version_checks
+        name: Version checks
+        language: system
+        entry: >
+          ./version_check.sh
+        always_run: true
+        fail_fast: true
+        pass_filenames: false

.prettierignore

@@ -15,5 +15,4 @@ __pycache__
 *.stdout
 *.stderr
 
-.literature
 pangene-test/

CHANGELOG.md

@@ -0,0 +1,63 @@
+# PlantandFoodResearch/pangene: Changelog
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## 0.3.0 - [30-April-2024]
+
+### `Added`
+
+1. Added changelog and semantic versioning
+2. Changed license to MIT
+3. Updated `.editorconfig`
+4. Moved .literature to test/ branch
+5. Renamed `pangene_local` to `local_pangene`
+6. Renamed `pangene_pfr` to `pfr_pangene`
+7. Added versioning checking
+8. Updated github workflow to use pre-commit instead of prettier and editorconfig check
+9. Added central singularity cache dir for pfr config
+10. Added `SORTMERNA_INDEX` before `SORTMERNA`
+11. Fixed sample contamination bug introduced by `file.simpleName`
+12. Now using empty files for stub testing in CI
+13. Now BRAKER can be skipped by including BRAKER outputs from previous runs in the `target_assemblies` param
+14. Added `gffcompare` to merge liftoff annotations
+15. Renamed `samplesheet` param to `fastq`
+16. Now using assemblysheet in combination with nf-validation for assembly input
+17. Added nextflow_schema.json
+18. Now using nf-validation to validate fastqsheet provided by params.fastq
+19. Moved `manifest.config` and `reporting_defaults.config` content to `nextflow.config`
+20. Now using a txt file for `params.external_protein_fastas`
+21. Now using nf-validation for `params.liftoff_annotations`
+22. Now using nf-validation for all the parameters
+23. Added `PURGE_BREAKER_MODELS` sub-workflow
+24. Added `GFF_EGGNOGMAPPER` sub-workflow
+25. Now using a custom version of `GFFREAD` which supports `meta` and `fasta`
+26. Now using TSEBRA to purge models which do not have full intron support from BRAKER hints
+27. Added params `eggnogmapper_evalue` and `eggnogmapper_pident`
+28. Added `PURGE_NOHIT_BRAKER_MODELS` sub-workflow
+29. Now merging BRAKER and liftoff models before running eggnogmapper
+30. Added `GFF_MERGE_CLEANUP` sub-workflow
+31. Now using `description` field to store notes and textual annotations in the gff files
+32. Now using `mRNA` in place of `transcript` in gff files
+33. Now `eggnogmapper_purge_nohits` is set to `false` by default
+34. Added `GFF_STORE` sub workflow
+35. `external_protein_fastas` and `eggnogmapper_db_dir` are not mandatory parameters
+36. Added contributors
+37. Add a document for the pipeline parameters
+38. Updated `pfr_pangene` and `pfr/profile.config`
+39. Now using local tests/stub files for GitHub CI
+40. Now removing iso-forms left by TSEBRA using `AGAT_SPFILTERFEATUREFROMKILLLIST`
+41. Added `pyproject.toml`
+42. Now using PFAMs from eggnog if description is '-'
+
+### `Fixed`
+
+1. Removed liftoff models with `valid_ORF=False`
+2. Updated license text to include 'Copyright (c) 2024 The New Zealand Institute for Plant and Food Research Limited'
+
+### `Dependencies`
+
+1. NextFlow!>=23.04.4
+2. nf-validation=1.1.3
+
+### `Deprecated`