Merge pull request #471 from LilyAnderssonLee/download-pipeline-bug

Remove stub run in download_pipeline.yml

.github/workflows/download_pipeline.yml

@@ -32,9 +32,6 @@ jobs:
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
 
-      - name: Disk space cleanup
-        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
-
       - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
           python-version: "3.12"
@@ -70,18 +67,8 @@ jobs:
       - name: Inspect download
         run: tree ./${{ env.REPOTITLE_LOWERCASE }}
 
-      - name: Run the downloaded pipeline (stub)
-        id: stub_run_pipeline
-        continue-on-error: true
-        env:
-          NXF_SINGULARITY_CACHEDIR: ./
-          NXF_SINGULARITY_HOME_MOUNT: true
-        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
-
-      - name: Run the downloaded pipeline (stub run not supported)
-        id: run_pipeline
-        if: ${{ job.steps.stub_run_pipeline.status == failure() }}
+      - name: Run the downloaded pipeline
         env:
           NXF_SINGULARITY_CACHEDIR: ./
           NXF_SINGULARITY_HOME_MOUNT: true
-        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results
+        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test_nothing,singularity --outdir ./results

CHANGELOG.md

@@ -3,14 +3,15 @@
 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).
 
-## v1.1.6 - Augmented Akita Patch [2024-04-12]
+## v1.1.6 - Augmented Akita Patch [2024-04-16]
 
 ### `Added`
 
 - [#454](https://github.com/nf-core/taxprofiler/pull/454) Updated to nf-core pipeline template v2.13.1 (added by @LilyAnderssonLee & @sofstam)
 - [#461](https://github.com/nf-core/taxprofiler/pull/461) Turned on 'strict' Nextflow evaluation runs (added by @jfy133)
 - [#461](https://github.com/nf-core/taxprofiler/pull/461) Optimised database compression so each compressed input database is untarred once, and shared amongst each run with different parameters (added by @jfy133)
 - [#461](https://github.com/nf-core/taxprofiler/pull/461) Added new parameter to optionally save uncompressed databases (added by @jfy133)
+- [#471](https://github.com/nf-core/taxprofiler/pull/471) Remove `-stub` run in the `download_pipeline.yml` because the pipeline does not support stub runs on dev (fixed by @LilyAnderssonLee)
 
 ### `Fixed`