adding a unifire subworkflow

.editorconfig

@@ -35,3 +35,12 @@ indent_style = unset
 # ignore ro-crate metadata files
 [**/ro-crate-metadata.json]
 insert_final_newline = unset
+
+# ignore the unifire fixtures
+[/modules/local/unifire/fixtures/**]
+charset = unset
+end_of_line = unset
+insert_final_newline = unset
+trim_trailing_whitespace = unset
+indent_size = unset
+indent_style = unset

.github/workflows/awsfulltest.yml

@@ -4,57 +4,39 @@ name: nf-core AWS full size tests
 # It runs the -profile 'test_full' on AWS batch
 
 on:
-  pull_request:
-    branches:
-      - main
-      - master
   workflow_dispatch:
   pull_request_review:
     types: [submitted]
+  release:
+    types: [published]
 
 jobs:
   run-platform:
     name: Run AWS full tests
-    # run only if the PR is approved by at least 2 reviewers and against the master branch or manually triggered
-    if: github.repository == 'nf-core/rnavar' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch'
+    # run only if the PR is approved by at least 2 reviewers and against the master/main branch or manually triggered
+    if: github.repository == 'nf-core/proteinannotator' && github.event.review.state == 'approved' && (github.event.pull_request.base.ref == 'master' || github.event.pull_request.base.ref == 'main') || github.event_name == 'workflow_dispatch'
     runs-on: ubuntu-latest
     steps:
-      - name: Get PR reviews
-        uses: octokit/request-action@v2.x
-        if: github.event_name != 'workflow_dispatch'
-        id: check_approvals
-        continue-on-error: true
-        with:
-          route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews?per_page=100
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-
-      - name: Check for approvals
-        if: ${{ failure() && github.event_name != 'workflow_dispatch' }}
-        run: |
-          echo "No review approvals found. At least 2 approvals are required to run this action automatically."
-          exit 1
-
-      - name: Check for enough approvals (>=2)
-        id: test_variables
-        if: github.event_name != 'workflow_dispatch'
+      - name: Set revision variable
+        id: revision
         run: |
-          JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}'
-          CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length')
-          test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required
+          echo "revision={%- raw -%}${{ (github.event_name == 'workflow_dispatch' || github.event_name == 'release') && github.sha || 'dev' }}" >> "$GITHUB_OUTPUT"
 
       - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
+        # TODO nf-core: You can customise AWS full pipeline tests as required
+        # Add full size test data (but still relatively small datasets for few samples)
+        # on the `test_full.config` test runs with only one set of parameters
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
-          revision: ${{ github.sha }}
-          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnavar/work-${{ github.sha }}
+          revision: ${{ steps.revision.outputs.revision }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}{% endraw %}/work/proteinannotator/{% raw %}work-${{ steps.revision.outputs.revision }}{% endraw %}
           parameters: |
             {
-              "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnavar/results-${{ github.sha }}"
+              "hook_url": "{% raw %}${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}{% endraw %}",
+              "outdir": "s3://{% raw %}${{ secrets.AWS_S3_BUCKET }}{% endraw %}/proteinannotator/{% raw %}results-${{ steps.revision.outputs.revision }}{% endraw %}"
             }
           profiles: test_full
 

.nf-core.yml

@@ -7,7 +7,7 @@ lint:
     - docs/images/nf-core-proteinannotator_logo_light.png
     - docs/images/nf-core-proteinannotator_logo_dark.png
     - .github/PULL_REQUEST_TEMPLATE.md
-nf_core_version: 3.2.0
+nf_core_version: 3.2.1
 repository_type: pipeline
 
 template:

CHANGELOG.md

@@ -12,6 +12,14 @@ Initial release of nf-core/proteinannotator, created with the [nf-core](https://
 - [[PR #42](https://github.com/nf-core/proteinannotator/pull/42)] Updated to `nf-test` on GitHub Actions and in the `PULL_REQUEST_TEMPLATE.md`
 - [[PR #13](https://github.com/nf-core/proteinannotator/pull/13)] Add nf-core seqkit/stats module
 
+- [[PR #45]](https://github.com/nf-core/proteinannotator/pull/45) Add the Unifire modules and subworkflow. Note that the docker
+  image is served from a personal repository,
+  the pirsr call in the unifire workflow does not work due to a bug in a dependency of the
+  unifire software (it is skipped via a parameter), and the update lineage script
+  had to be slightly modified and placed in a
+  template due to a typo in the original script. The unifire maintainers are aware, but
+  in the meantime, this workflow can be used.
+
 ### `Fixed`
 
 ### `Dependencies`

modules.json

@@ -24,6 +24,11 @@
                         "branch": "master",
                         "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
                         "installed_by": ["modules"]
+                    },
+                    "untar": {
+                        "branch": "master",
+                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
+                        "installed_by": ["modules"]
                     }
                 }
             },