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restore changes to testing (removes podman discussed in nf-core#2675)
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TomKellyGenetics committed Dec 16, 2022
1 parent 47ea08b commit a2626fb
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Showing 2 changed files with 1 addition and 10 deletions.
7 changes: 1 addition & 6 deletions .github/workflows/pytest-workflow.yml
Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@ jobs:
fail-fast: false
matrix:
tags: ["${{ fromJson(needs.changes.outputs.modules) }}"]
profile: ["docker", "singularity", "podman"]
profile: ["docker", "singularity", "conda"]
exclude:
- profile: "conda"
tags: bases2fastq
Expand Down Expand Up @@ -121,11 +121,6 @@ jobs:
with:
singularity-version: 3.7.1

- name: Set up Podman
if: matrix.profile == 'podman'
run: |
sudo ln -sf /usr/bin/podman /usr/bin/docker
- name: Set up miniconda
if: matrix.profile == 'conda'
uses: conda-incubator/setup-miniconda@v2
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4 changes: 0 additions & 4 deletions tests/config/nextflow.config
Original file line number Diff line number Diff line change
Expand Up @@ -18,12 +18,8 @@ if ("$PROFILE" == "singularity") {
} else if ("$PROFILE" == "mamba") {
conda.enabled = true
conda.useMamba = true
} else if ("$PROFILE" == "podman") {
podman.enabled = true
podman.runOptions = "--runtime /usr/bin/crun --userns=keep-id --platform linux/x86_64"
} else {
docker.enabled = true
docker.fixOwnership = true
docker.userEmulation = true
docker.runOptions = "--platform linux/x86_64"
}
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