diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 41f5c11..bcbb910 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -28,6 +28,3 @@ jobs: "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/taxprofiler/results-${{ github.sha }}" } profiles: test_full,aws_tower - nextflow_config: | - process.errorStrategy = 'retry' - process.maxRetries = 3 diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index ebffec6..5d35eea 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -23,6 +23,3 @@ jobs: "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/taxprofiler/results-test-${{ github.sha }}" } profiles: test,aws_tower - nextflow_config: | - process.errorStrategy = 'retry' - process.maxRetries = 3 diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml index b8a412e..b5b9ae2 100644 --- a/.github/workflows/branch.yml +++ b/.github/workflows/branch.yml @@ -13,7 +13,7 @@ jobs: - name: Check PRs if: github.repository == 'nf-core/taxprofiler' run: | - "{ [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/taxprofiler ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]" + { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/taxprofiler ]] && [[ $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 -# diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 7bb2076..689a193 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -71,5 +71,3 @@ jobs: # Remember that you can parallelise this by using strategy.matrix run: | nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }} - -# diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml new file mode 100644 index 0000000..5a5f775 --- /dev/null +++ b/.github/workflows/fix-linting.yml @@ -0,0 +1,55 @@ +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/taxprofiler' + 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 diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index e9cf5de..77358de 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -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 - -# diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index 91c487a..04758f6 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -26,4 +26,3 @@ jobs: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} number: ${{ steps.pr_number.outputs.pr_number }} path: linting-logs/lint_results.md -# diff --git a/.prettierignore b/.prettierignore index c037321..2fd5fd6 100644 --- a/.prettierignore +++ b/.prettierignore @@ -1,2 +1,10 @@ +email_template.html +.nextflow* +work/ +data/ +results/ +.DS_Store testing/ +testing* tests/ +*.pyc diff --git a/README.md b/README.md index 66578e5..722cccb 100644 --- a/README.md +++ b/README.md @@ -2,17 +2,18 @@ [![GitHub Actions CI Status](https://github.com/nf-core/taxprofiler/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/taxprofiler/actions?query=workflow%3A%22nf-core+CI%22) [![GitHub Actions Linting Status](https://github.com/nf-core/taxprofiler/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/taxprofiler/actions?query=workflow%3A%22nf-core+linting%22) -[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/taxprofiler/results) -[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) +[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?logo=Amazon%20AWS)](https://nf-co.re/taxprofiler/results) +[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8)](https://doi.org/10.5281/zenodo.XXXXXXX) -[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg?labelColor=000000)](https://www.nextflow.io/) -[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) -[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) -[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) +[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg)](https://www.nextflow.io/) +[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?logo=anaconda)](https://docs.conda.io/en/latest/) +[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?logo=docker)](https://www.docker.com/) +[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg)](https://sylabs.io/docs/) +[![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/taxprofiler) -[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23taxprofiler-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/taxprofiler) -[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core) -[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core) +[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23taxprofiler-4A154B?logo=slack)](https://nfcore.slack.com/channels/taxprofiler) +[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?logo=twitter)](https://twitter.com/nf_core) +[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?logo=youtube)](https://www.youtube.com/c/nf-core) ## Introduction diff --git a/assets/email_template.html b/assets/email_template.html index c8dce51..f40addd 100644 --- a/assets/email_template.html +++ b/assets/email_template.html @@ -1,111 +1,53 @@ - - - - + + + + - - - nf-core/taxprofiler Pipeline Report - - -
- + + nf-core/taxprofiler Pipeline Report + + +
-

nf-core/taxprofiler v${version}

-

Run Name: $runName

+ - <% if (!success){ out << """ -
-

nf-core/taxprofiler execution completed unsuccessfully!

+

nf-core/taxprofiler v${version}

+

Run Name: $runName

+ +<% if (!success){ + out << """ +
+

nf-core/taxprofiler execution completed unsuccessfully!

The exit status of the task that caused the workflow execution to fail was: $exitStatus.

The full error message was:

- 
${errorReport}
-
- """ } else { out << """ -
- nf-core/taxprofiler execution completed successfully! -
- """ } %> - -

The workflow was completed at $dateComplete (duration: $duration)

-

The command used to launch the workflow was as follows:

- 
-$commandLine
- -

Pipeline Configuration:

- - - <% out << summary.collect{ k,v -> " - - - - - " }.join("\n") %> - -
- $k - - 
$v
-
- -

nf-core/taxprofiler

-

https://github.com/nf-core/taxprofiler

+ 
${errorReport}
- + """ +} else { + out << """ +
+ nf-core/taxprofiler execution completed successfully! +
+ """ +} +%> + +

The workflow was completed at $dateComplete (duration: $duration)

+

The command used to launch the workflow was as follows:

+
$commandLine
+ +

Pipeline Configuration:

+ + + <% out << summary.collect{ k,v -> "" }.join("\n") %> + +
$k
$v
+ +

nf-core/taxprofiler

+

https://github.com/nf-core/taxprofiler

+ +
+ + diff --git a/nextflow.config b/nextflow.config index 4bcb1b1..f55bc84 100644 --- a/nextflow.config +++ b/nextflow.config @@ -226,7 +226,7 @@ trace { } dag { enabled = true - file = "${params.tracedir}/pipeline_dag_${trace_timestamp}.svg" + file = "${params.tracedir}/pipeline_dag_${trace_timestamp}.html" } manifest {