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fix: add suggestions from reviews
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11
.github/CONTRIBUTING.md
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@ -18,10 +18,9 @@ If you'd like to write some code for nf-core/modules, the standard workflow is a
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1. Check that there isn't already an issue about your idea in the [nf-core/modules issues](https://github.com/nf-core/modules/issues) to avoid duplicating work
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* If there isn't one already, please create one so that others know you're working on this
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2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/modules repository](https://github.com/nf-core/modules) to your GitHub account
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3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions)
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4. When adding a module file, follow the [guidelines](https://github.com/nf-core/modules#adding-a-new-module-file)
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5. Ensure that [tests are working locally](https://github.com/nf-core/modules#running-tests-locally)
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6. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged
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3. When adding a module file, follow the [guidelines](https://github.com/nf-core/modules#adding-a-new-module-file)
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4. Ensure that [tests are working locally](https://github.com/nf-core/modules#running-tests-locally)
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5. Submit a Pull Request against the `master` branch and wait for the code to be reviewed and merged
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If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/).
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@ -56,13 +55,13 @@ If you add a new module, please ensure you add the information of the tool.
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Add to the script block of the process, something like the following:
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```bash
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<YOUR_TOOL> --version &> v_<YOUR_TOOL>.txt 2>&1 || true
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<YOUR_TOOL> --version &> v_<YOUR_TOOL>.txt 2>&1
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```
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or
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```bash
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<YOUR_TOOL> --help | head -n 1 &> v_<YOUR_TOOL>.txt 2>&1 || true
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<YOUR_TOOL> --help | head -n 1 &> v_<YOUR_TOOL>.txt 2>&1
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```
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### Images and figures
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6
.github/PULL_REQUEST_TEMPLATE.md
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.github/PULL_REQUEST_TEMPLATE.md
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@ -15,8 +15,8 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/modu
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- [ ] This comment contains a description of changes (with reason).
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- [ ] If you've fixed a bug or added code that should be tested, add tests!
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- [ ] If you've added a new tool - have you followed the module conventions in the [contribution docs](https://github.com/nf-core/modules/tree/master/.github/CONTRIBUTING.md)
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- [ ] If necessary, include test data in your PR.
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- [ ] If you've added a new tool - have you followed the module conventions in the [contribution docs](https://github.com/nf-core/modules/tree/master/.github/CONTRIBUTING.md)
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- [ ] If necessary, include test data in your PR.
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- [ ] Remove all TODO statements.
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- [ ] Emit the `<SOFTWARE>.version.txt` file.
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- [ ] Follow the naming conventions.
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@ -25,3 +25,5 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/modu
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- [ ] Add a resource `label`
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- [ ] Use BioConda and BioContainers if possible to fulfil software requirements.
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- [ ] Ensure that the test works (`PROFILE=docker pytest --tag <MODULE> --symlink --wt 2 --keep-workflow-wd`)
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- [ ] Ensure that the test works (`PROFILE=singularity pytest --tag <MODULE> --symlink --wt 2 --keep-workflow-wd`)
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- [ ] Ensure that the test works (`PROFILE=conda pytest --tag <MODULE> --symlink --wt 2 --keep-workflow-wd`)
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