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Merge pull request #81 from nf-core/nf-core-template-merge-2.4

Important! Template update for nf-core/tools v2.4
This commit is contained in:
James A. Fellows Yates 2022-05-19 11:00:48 +01:00 committed by GitHub
commit ba75685550
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11 changed files with 121 additions and 127 deletions

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

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

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@ -13,7 +13,7 @@ jobs:
- name: Check PRs - name: Check PRs
if: github.repository == 'nf-core/taxprofiler' if: github.repository == 'nf-core/taxprofiler'
run: | 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 # 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 # 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! Thanks again for your contribution!
repo-token: ${{ secrets.GITHUB_TOKEN }} repo-token: ${{ secrets.GITHUB_TOKEN }}
allow-repeats: false allow-repeats: false
#

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@ -71,5 +71,3 @@ jobs:
# Remember that you can parallelise this by using strategy.matrix # Remember that you can parallelise this by using strategy.matrix
run: | run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }} nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }}
#

55
.github/workflows/fix-linting.yml vendored Normal file
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@ -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

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@ -48,7 +48,7 @@ jobs:
wget -qO- get.nextflow.io | bash wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/ sudo mv nextflow /usr/local/bin/
- uses: actions/setup-python@v1 - uses: actions/setup-python@v3
with: with:
python-version: "3.6" python-version: "3.6"
architecture: "x64" architecture: "x64"
@ -78,5 +78,3 @@ jobs:
lint_log.txt lint_log.txt
lint_results.md lint_results.md
PR_number.txt PR_number.txt
#

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@ -26,4 +26,3 @@ jobs:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
number: ${{ steps.pr_number.outputs.pr_number }} number: ${{ steps.pr_number.outputs.pr_number }}
path: linting-logs/lint_results.md path: linting-logs/lint_results.md
#

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@ -1,2 +1,10 @@
email_template.html
.nextflow*
work/
data/
results/
.DS_Store
testing/ testing/
testing*
tests/ tests/
*.pyc

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@ -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 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) [![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) [![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?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) [![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/) [![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?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![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?labelColor=000000&logo=docker)](https://www.docker.com/) [![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?labelColor=000000)](https://sylabs.io/docs/) [![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) [![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?labelColor=000000&logo=twitter)](https://twitter.com/nf_core) [![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?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core) [![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?logo=youtube)](https://www.youtube.com/c/nf-core)
## Introduction ## Introduction

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@ -1,111 +1,53 @@
<html> <html>
<head> <head>
<meta charset="utf-8" /> <meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge" /> <meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1" /> <meta name="viewport" content="width=device-width, initial-scale=1">
<!-- prettier-ignore --> <meta name="description" content="nf-core/taxprofiler: Taxonomic profiling of shotgun metagenomic data">
<meta name="description" content="nf-core/taxprofiler: Taxonomic profiling of shotgun metagenomic data" />
<title>nf-core/taxprofiler Pipeline Report</title> <title>nf-core/taxprofiler Pipeline Report</title>
</head> </head>
<body> <body>
<div style="font-family: Helvetica, Arial, sans-serif; padding: 30px; max-width: 800px; margin: 0 auto"> <div style="font-family: Helvetica, Arial, sans-serif; padding: 30px; max-width: 800px; margin: 0 auto;">
<img src="cid:nfcorepipelinelogo" />
<img src="cid:nfcorepipelinelogo">
<h1>nf-core/taxprofiler v${version}</h1> <h1>nf-core/taxprofiler v${version}</h1>
<h2>Run Name: $runName</h2> <h2>Run Name: $runName</h2>
<% if (!success){ out << """ <% if (!success){
<div out << """
style=" <div style="color: #a94442; background-color: #f2dede; border-color: #ebccd1; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
color: #a94442; <h4 style="margin-top:0; color: inherit;">nf-core/taxprofiler execution completed unsuccessfully!</h4>
background-color: #f2dede;
border-color: #ebccd1;
padding: 15px;
margin-bottom: 20px;
border: 1px solid transparent;
border-radius: 4px;
"
>
<h4 style="margin-top: 0; color: inherit">nf-core/taxprofiler execution completed unsuccessfully!</h4>
<p>The exit status of the task that caused the workflow execution to fail was: <code>$exitStatus</code>.</p> <p>The exit status of the task that caused the workflow execution to fail was: <code>$exitStatus</code>.</p>
<p>The full error message was:</p> <p>The full error message was:</p>
<pre style="white-space: pre-wrap; overflow: visible; margin-bottom: 0">${errorReport}</pre> <pre style="white-space: pre-wrap; overflow: visible; margin-bottom: 0;">${errorReport}</pre>
</div> </div>
""" } else { out << """ """
<div } else {
style=" out << """
color: #3c763d; <div style="color: #3c763d; background-color: #dff0d8; border-color: #d6e9c6; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
background-color: #dff0d8;
border-color: #d6e9c6;
padding: 15px;
margin-bottom: 20px;
border: 1px solid transparent;
border-radius: 4px;
"
>
nf-core/taxprofiler execution completed successfully! nf-core/taxprofiler execution completed successfully!
</div> </div>
""" } %> """
}
%>
<p>The workflow was completed at <strong>$dateComplete</strong> (duration: <strong>$duration</strong>)</p> <p>The workflow was completed at <strong>$dateComplete</strong> (duration: <strong>$duration</strong>)</p>
<p>The command used to launch the workflow was as follows:</p> <p>The command used to launch the workflow was as follows:</p>
<pre <pre style="white-space: pre-wrap; overflow: visible; background-color: #ededed; padding: 15px; border-radius: 4px; margin-bottom:30px;">$commandLine</pre>
style="
white-space: pre-wrap;
overflow: visible;
background-color: #ededed;
padding: 15px;
border-radius: 4px;
margin-bottom: 30px;
"
>
$commandLine</pre
>
<h3>Pipeline Configuration:</h3> <h3>Pipeline Configuration:</h3>
<table <table style="width:100%; max-width:100%; border-spacing: 0; border-collapse: collapse; border:0; margin-bottom: 30px;">
style=" <tbody style="border-bottom: 1px solid #ddd;">
width: 100%; <% out << summary.collect{ k,v -> "<tr><th style='text-align:left; padding: 8px 0; line-height: 1.42857143; vertical-align: top; border-top: 1px solid #ddd;'>$k</th><td style='text-align:left; padding: 8px; line-height: 1.42857143; vertical-align: top; border-top: 1px solid #ddd;'><pre style='white-space: pre-wrap; overflow: visible;'>$v</pre></td></tr>" }.join("\n") %>
max-width: 100%;
border-spacing: 0;
border-collapse: collapse;
border: 0;
margin-bottom: 30px;
"
>
<tbody style="border-bottom: 1px solid #ddd">
<% out << summary.collect{ k,v -> "
<tr>
<th
style="
text-align: left;
padding: 8px 0;
line-height: 1.42857143;
vertical-align: top;
border-top: 1px solid #ddd;
"
>
$k
</th>
<td
style="
text-align: left;
padding: 8px;
line-height: 1.42857143;
vertical-align: top;
border-top: 1px solid #ddd;
"
>
<pre style="white-space: pre-wrap; overflow: visible">$v</pre>
</td>
</tr>
" }.join("\n") %>
</tbody> </tbody>
</table> </table>
<p>nf-core/taxprofiler</p> <p>nf-core/taxprofiler</p>
<p><a href="https://github.com/nf-core/taxprofiler">https://github.com/nf-core/taxprofiler</a></p> <p><a href="https://github.com/nf-core/taxprofiler">https://github.com/nf-core/taxprofiler</a></p>
</div> </div>
</body> </body>
</html> </html>

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@ -226,7 +226,7 @@ trace {
} }
dag { dag {
enabled = true enabled = true
file = "${params.tracedir}/pipeline_dag_${trace_timestamp}.svg" file = "${params.tracedir}/pipeline_dag_${trace_timestamp}.html"
} }
manifest { manifest {