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Fix name
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maxulysse committed Oct 10, 2024
1 parent a1ff5e9 commit 45012dd
Showing 1 changed file with 7 additions and 7 deletions.
14 changes: 7 additions & 7 deletions nf_core/pipeline-template/.github/workflows/ci.yml
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ env:
NXF_SINGULARITY_CACHEDIR: {% raw %}${{ github.workspace }}{% endraw %}/.singularity
NXF_SINGULARITY_LIBRARYDIR: {% raw %}${{ github.workspace }}{% endraw %}/.singularity

concurrency:
concurrency:
group: "{% raw %}${{ github.workflow }}{% endraw %}-{% raw %}${{ github.event.pull_request.number || github.ref }}{% endraw %}"
cancel-in-progress: true

Expand Down Expand Up @@ -47,12 +47,12 @@ jobs:
- name: Check out pipeline code
uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4

- name: Install Nextflow
- name: Set up Nextflow
uses: nf-core/setup-nextflow@v2
with:
version: "{% raw %}${{ matrix.NXF_VER }}{% endraw %}"

- name: Setup apptainer
- name: Set up Apptainer
if: matrix.profile == 'singularity'
uses: eWaterCycle/setup-apptainer@main

Expand All @@ -62,15 +62,15 @@ jobs:
mkdir -p $NXF_SINGULARITY_CACHEDIR
mkdir -p $NXF_SINGULARITY_LIBRARYDIR
- name: Set up miniconda
- name: Set up Miniconda
if: matrix.profile == 'conda'
uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3
with:
miniconda-version: "latest"
auto-update-conda: true
channels: conda-forge,bioconda

- name: Conda setup
- name: Set up Conda
if: matrix.profile == 'conda'
run: |
conda clean -a
Expand All @@ -79,9 +79,9 @@ jobs:
echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
echo $(realpath python) >> $GITHUB_PATH
- name: Disk space cleanup
- name: Clean up Disk space
uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1

- name: " Run pipeline with test data {% raw %}${{ matrix.NXF_VER }}{% endraw %} | {% raw %}${{ matrix.test }}{% endraw %} | {% raw %}${{ matrix.profile }}{% endraw %}"
- name: "Run pipeline with test data {% raw %}${{ matrix.NXF_VER }}{% endraw %} | {% raw %}${{ matrix.test }}{% endraw %} | {% raw %}${{ matrix.profile }}{% endraw %}"
run: |
nextflow run ${GITHUB_WORKSPACE} -profile {% raw %}${{ matrix.test }}{% endraw %},{% raw %}${{ matrix.profile }}{% endraw %} --outdir ./results

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