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Merge pull request #244 from grst/fix-conda

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Only use one thread for pytest-workflow
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Gregor Sturm 2021-02-23 14:15:05 +01:00 committed by GitHub
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3 changed files with 8 additions and 7 deletions
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6
.github/PULL_REQUEST_TEMPLATE.md vendored
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@ -25,6 +25,6 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/modu
- [ ] Add a resource `label` - [ ] Add a resource `label`
- [ ] Use BioConda and BioContainers if possible to fulfil software requirements. - [ ] Use BioConda and BioContainers if possible to fulfil software requirements.
- Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky: - Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
- [ ] `PROFILE=docker pytest --tag <MODULE> --symlink --wt 2 --keep-workflow-wd` - [ ] `PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd`
- [ ] `PROFILE=singularity pytest --tag <MODULE> --symlink --wt 2 --keep-workflow-wd` - [ ] `PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd`
- [ ] `PROFILE=conda pytest --tag <MODULE> --symlink --wt 2 --keep-workflow-wd` - [ ] `PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd`

3
.github/workflows/pytest-workflow.yml vendored
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@ -80,7 +80,8 @@ jobs:
# Test the module # Test the module
- name: Run pytest-workflow - name: Run pytest-workflow
run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --wt 2 --kwdof # only use one thread for pytest-workflow to avoid race condition on conda cache.
run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof
- name: Upload logs on failure - name: Upload logs on failure
if: failure() if: failure()

6
README.md
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@ -275,21 +275,21 @@ In order to test that each module added to `nf-core/modules` is actually working
```console ```console
cd /path/to/git/clone/of/nf-core/modules/ cd /path/to/git/clone/of/nf-core/modules/
PROFILE=docker pytest --tag bowtie --symlink --wt 2 --keep-workflow-wd PROFILE=docker pytest --tag bowtie --symlink --keep-workflow-wd
``` ```
- Typical command with Singularity: - Typical command with Singularity:
```console ```console
cd /path/to/git/clone/of/nf-core/modules/ cd /path/to/git/clone/of/nf-core/modules/
TMPDIR=~ PROFILE=singularity pytest --tag bowtie --symlink --wt 2 --keep-workflow-wd TMPDIR=~ PROFILE=singularity pytest --tag bowtie --symlink --keep-workflow-wd
``` ```
- Typical command with Conda: - Typical command with Conda:
```console ```console
cd /path/to/git/clone/of/nf-core/modules/ cd /path/to/git/clone/of/nf-core/modules/
PROFILE=conda pytest --tag bowtie --symlink --wt 2 --keep-workflow-wd PROFILE=conda pytest --tag bowtie --symlink --keep-workflow-wd
``` ```
- See [docs on running pytest-workflow](https://pytest-workflow.readthedocs.io/en/stable/#running-pytest-workflow) for more info. - See [docs on running pytest-workflow](https://pytest-workflow.readthedocs.io/en/stable/#running-pytest-workflow) for more info.