Merge pull request #124 from luslab/dev (b1888c3b) · Commits · Chaos / Cutandrun

.github/workflows/awsfulltest.yml

+0 −3

Original line number	Diff line number	Diff line
		@@ -28,6 +28,3 @@ jobs:
		"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/cutandrun/results-${{ github.sha }}"
		}
		profiles: test_full,aws_tower
		nextflow_config: \|
		process.errorStrategy = 'retry'
		process.maxRetries = 3

+0 −3

Original line number	Diff line number	Diff line
		@@ -23,6 +23,3 @@ jobs:
		"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/cutandrun/results-test-${{ github.sha }}"
		}
		profiles: test,aws_tower
		nextflow_config: \|
		process.errorStrategy = 'retry'
		process.maxRetries = 3

+1 −2

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		@@ -13,7 +13,7 @@ jobs:
		- name: Check PRs
		if: github.repository == 'nf-core/cutandrun'
		run: \|
		"{ [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/cutandrun ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } \|\| [[ $GITHUB_HEAD_REF == "patch" ]]"
		{ [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/cutandrun ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } \|\| [[ $GITHUB_HEAD_REF == "patch" ]]

		# If the above check failed, post a comment on the PR explaining the failure
		# NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
		@@ -42,4 +42,3 @@ jobs:
		Thanks again for your contribution!
		repo-token: ${{ secrets.GITHUB_TOKEN }}
		allow-repeats: false
		#

0 → 100644

+55 −0

Original line number	Diff line number	Diff line
		name: Fix linting from a comment
		on:
		issue_comment:
		types: [created]

		jobs:
		deploy:
		# Only run if comment is on a PR with the main repo, and if it contains the magic keywords
		if: >
		contains(github.event.comment.html_url, '/pull/') &&
		contains(github.event.comment.body, '@nf-core-bot fix linting') &&
		github.repository == 'nf-core/cutandrun'
		runs-on: ubuntu-latest
		steps:
		# Use the @nf-core-bot token to check out so we can push later
		- uses: actions/checkout@v3
		with:
		token: ${{ secrets.nf_core_bot_auth_token }}

		# Action runs on the issue comment, so we don't get the PR by default
		# Use the gh cli to check out the PR
		- name: Checkout Pull Request
		run: gh pr checkout ${{ github.event.issue.number }}
		env:
		GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}

		- uses: actions/setup-node@v2

		- name: Install Prettier
		run: npm install -g prettier @prettier/plugin-php

		# Check that we actually need to fix something
		- name: Run 'prettier --check'
		id: prettier_status
		run: \|
		if prettier --check ${GITHUB_WORKSPACE}; then
		echo "::set-output name=result::pass"
		else
		echo "::set-output name=result::fail"
		fi

		- name: Run 'prettier --write'
		if: steps.prettier_status.outputs.result == 'fail'
		run: prettier --write ${GITHUB_WORKSPACE}

		- name: Commit & push changes
		if: steps.prettier_status.outputs.result == 'fail'
		run: \|
		git config user.email "core@nf-co.re"
		git config user.name "nf-core-bot"
		git config push.default upstream
		git add .
		git status
		git commit -m "[automated] Fix linting with Prettier"
		git push

+1 −3

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		@@ -48,7 +48,7 @@ jobs:
		wget -qO- get.nextflow.io \| bash
		sudo mv nextflow /usr/local/bin/

		- uses: actions/setup-python@v1
		- uses: actions/setup-python@v3
		with:
		python-version: "3.6"
		architecture: "x64"
		@@ -78,5 +78,3 @@ jobs:
		lint_log.txt
		lint_results.md
		PR_number.txt

		#