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Remove stub run in download_pipeline.yml #471

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merged 4 commits into from
Apr 16, 2024
Merged

Remove stub run in download_pipeline.yml #471

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8941b6e
manully define stub run branch is master
LilyAnderssonLee Apr 12, 2024
2db93e4
update changelog and remove disk clean in download_pipeline.yml
LilyAnderssonLee Apr 12, 2024
39a66a3
Update download_pipeline.yml
LilyAnderssonLee Apr 12, 2024
8fe3968
remove stub run in download pipeline
LilyAnderssonLee Apr 16, 2024
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17 changes: 2 additions & 15 deletions .github/workflows/download_pipeline.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -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"
Expand Down Expand Up @@ -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
3 changes: 2 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -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`

Expand Down
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