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Testing so we can see priv levels
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DLBPointon committed Dec 12, 2024
1 parent d5b7a1e commit e611af4
Showing 1 changed file with 28 additions and 37 deletions.
65 changes: 28 additions & 37 deletions .github/workflows/ci.yml
Original file line number Diff line number Diff line change
Expand Up @@ -35,47 +35,38 @@ jobs:
id: branch-names
uses: tj-actions/branch-names@v8

# - name: Install Nextflow
# uses: nf-core/setup-nextflow@v2
# with:
# version: "${{ matrix.NXF_VER }}"
- name: Install Nextflow
uses: nf-core/setup-nextflow@v2
with:
version: "${{ matrix.NXF_VER }}"

- name: Setup apptainer
uses: eWaterCycle/setup-apptainer@main

- name: Get privilege Level
- name: Set up Singularity
run: |
grep -q 'kernel.unprivileged_userns_clone=1' /etc/sysctl.d/90-unprivileged_userns.conf && \
echo "User namespaces enabled, continue the Apptainer installation" || \
echo "User namespaces NOT enabled, your use of Apptainer will be very limited"
# - name: Set up Singularity
# run: |
# mkdir -p $NXF_SINGULARITY_CACHEDIR
# mkdir -p $NXF_SINGULARITY_LIBRARYDIR
mkdir -p $NXF_SINGULARITY_CACHEDIR
mkdir -p $NXF_SINGULARITY_LIBRARYDIR
# - name: Install Python
# uses: actions/setup-python@v5
# with:
# python-version: "3.10"
- name: Install Python
uses: actions/setup-python@v5
with:
python-version: "3.10"

# - name: Install nf-core
# run: |
# pip install nf-core
- name: Install nf-core
run: |
pip install nf-core
# - name: NF-Core Download - download singularity containers
# # Forcibly download repo on active branch and download SINGULARITY containers into the CACHE dir if not found
# # Must occur after singularity install or will crash trying to dl containers
# # Zip up this fresh download and run the checked out version
# run: |
# nf-core download sanger-tol/treeval --revision ${{ steps.branch-names.outputs.current_branch }} --compress none -d --force --outdir sanger-treeval --container-cache-utilisation amend --container-system singularity
- name: NF-Core Download - download singularity containers
# Forcibly download repo on active branch and download SINGULARITY containers into the CACHE dir if not found
# Must occur after singularity install or will crash trying to dl containers
# Zip up this fresh download and run the checked out version
run: |
nf-core download sanger-tol/treeval --revision ${{ steps.branch-names.outputs.current_branch }} --compress none -d --force --outdir sanger-treeval --container-cache-utilisation amend --container-system singularity
# - name: Download Tiny test data
# # Download A fungal test data set that is full enough to show some real output.
# run: |
# curl https://tolit.cog.sanger.ac.uk/test-data/resources/treeval/TreeValTinyData.tar.gz | tar xzf -
- name: Download Tiny test data
# Download A fungal test data set that is full enough to show some real output.
run: |
curl https://tolit.cog.sanger.ac.uk/test-data/resources/treeval/TreeValTinyData.tar.gz | tar xzf -
# - name: Singularity - Run FULL pipeline with test data
# # Remember that you can parallelise this by using strategy.matrix
# run: |
# nextflow run ./sanger-treeval/${{ steps.branch-names.outputs.current_branch }}/main.nf -profile test_github,singularity --outdir ./Sing-Full
- name: Singularity - Run FULL pipeline with test data
# Remember that you can parallelise this by using strategy.matrix
run: |
nextflow run ./sanger-treeval/${{ steps.branch-names.outputs.current_branch }}/main.nf -profile test_github,docker --outdir ./Sing-Full

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