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Template: test pipeline with conda and singularity on PRs to master #3149

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merged 4 commits into from
Oct 1, 2024
Merged

Template: test pipeline with conda and singularity on PRs to master #3149

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a5718f7
test pipeline with conda and singularity on PRs to master
mirpedrol Aug 30, 2024
248b669
add workflow_dispatch to pipeline ci test
mirpedrol Aug 30, 2024
88f9735
update changelog
mirpedrol Aug 30, 2024
cd138ec
Merge branch 'dev' into pipeline-test-conda-syngularity
mirpedrol Oct 1, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -36,6 +36,7 @@
- add option to exclude documentation from pipeline template ([#3130](https://github.com/nf-core/tools/pull/3130))
- add option to exclude test configs from pipeline template ([#3133](https://github.com/nf-core/tools/pull/3133))
- add option to exclude tower.yml from pipeline template ([#3134](https://github.com/nf-core/tools/pull/3134))
- test pipeline with conda and singularity on PRs to master ([#3149](https://github.com/nf-core/tools/pull/3149))
- run nf-core lint `--release` on PRs to master ([#3148](https://github.com/nf-core/tools/pull/3148))
- Add tests to ensure all files are part of a template customisation group and all groups are tested ([#3099](https://github.com/nf-core/tools/pull/3099))
- Remove if/else block to include `igenomes.config` ([#3168](https://github.com/nf-core/tools/pull/3168))
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15 changes: 14 additions & 1 deletion nf_core/pipeline-template/.github/workflows/ci.yml
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Expand Up @@ -7,6 +7,7 @@ on:
pull_request:
release:
types: [published]
workflow_dispatch:

env:
NXF_ANSI_LOG: false
Expand Down Expand Up @@ -38,9 +39,21 @@ jobs:
- name: Disk space cleanup
uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1

- name: Run pipeline with test data
- name: Run pipeline with test data (docker)
# TODO nf-core: You can customise CI pipeline run tests as required
# For example: adding multiple test runs with different parameters
# Remember that you can parallelise this by using strategy.matrix
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results

- name: Run pipeline with test data (singularity)
# TODO nf-core: You can customise CI pipeline run tests as required
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,singularity --outdir ./results
if: "{% raw %}${{ github.base_ref == 'master' }}{% endraw %}"

- name: Run pipeline with test data (conda)
# TODO nf-core: You can customise CI pipeline run tests as required
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,conda --outdir ./results
if: "{% raw %}${{ github.base_ref == 'master' }}{% endraw %}"
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