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Fix download pipeline workflow #470

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Merged
merged 2 commits into from
Apr 12, 2024
Merged

Fix download pipeline workflow #470

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04a2ba7
update download-pipeline.yml
LilyAnderssonLee Apr 12, 2024
06d2985
update download-pipeline.yml
LilyAnderssonLee Apr 12, 2024
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11 changes: 8 additions & 3 deletions .github/workflows/download_pipeline.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,8 @@ on:
pull_request:
types:
- opened
- edited
- synchronize
branches:
- master
pull_request_target:
Expand All @@ -28,11 +30,14 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
uses: nf-core/setup-nextflow@v2

- name: Disk space cleanup
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I do not know where the jlumbroso/free-disk-space step comes from. I have not heard of any issues with disk space so far, and it does uninstall a lot of packages that may or may not be needed. Probably no harm done here, but I believe also not strictly necessary.

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I will keep it in mind in case it causes issues in the future.

uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1

- uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
with:
python-version: "3.11"
python-version: "3.12"
architecture: "x64"
- uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7
with:
Expand Down Expand Up @@ -79,4 +84,4 @@ jobs:
env:
NXF_SINGULARITY_CACHEDIR: ./
NXF_SINGULARITY_HOME_MOUNT: true
run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results{% endraw %}
run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results
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Exactly, that {% endraw %} did probably cause issues, because other than that you already have the most current version of the action with the fallback in case stub runs are not supported.

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