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GitHub Actions: add TODO statement to encourage customisation#488

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drpatelh merged 2 commits intonf-core:devfrom
ewels:todo-actions
Jan 27, 2020
Merged

GitHub Actions: add TODO statement to encourage customisation#488
drpatelh merged 2 commits intonf-core:devfrom
ewels:todo-actions

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@ewels ewels commented Jan 27, 2020

The CI tests should probably be customised to run with different parameters. Added a TODO statement that should be flagged as a warning by the linting code to encourage this.

@ewels ewels added template nf-core pipeline/component template linting labels Jan 27, 2020
@ewels ewels requested a review from a team January 27, 2020 11:14
@ewels ewels mentioned this pull request Jan 27, 2020
5 tasks
docker pull {{ cookiecutter.name_docker }}:dev && docker tag {{ cookiecutter.name_docker }}:dev {{ cookiecutter.name_docker }}:dev
- name: Run test
- name: Pull docker image
run: docker pull {{ cookiecutter.name_docker }}:dev && docker tag {{ cookiecutter.name_docker }}:dev {{ cookiecutter.name_docker }}:dev
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Suggested change
run: docker pull {{ cookiecutter.name_docker }}:dev && docker tag {{ cookiecutter.name_docker }}:dev {{ cookiecutter.name_docker }}:dev
run: |

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I think this is why the tests are failing. The docker command needs to be on its own line.

docker pull {{ cookiecutter.name_docker }}:dev && docker tag {{ cookiecutter.name_docker }}:dev {{ cookiecutter.name_docker }}:dev
- name: Run test
- name: Pull docker image
run: docker pull {{ cookiecutter.name_docker }}:dev && docker tag {{ cookiecutter.name_docker }}:dev {{ cookiecutter.name_docker }}:dev
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I think this is why the tests are failing. The docker command needs to be on its own line.

@drpatelh drpatelh merged commit 71df058 into nf-core:dev Jan 27, 2020
@ewels ewels deleted the todo-actions branch January 27, 2020 11:52
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ewels commented Jan 27, 2020

Thanks! It's not so much that it needs to be on its own line, but more than it needs to be escaped - the command has a : in it, so without quotes (or being a multiline string with |), it's interpreted as a YAML dictionary and breaks.

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