mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-24 02:29:55 +00:00
Template update for nf-core/tools version 2.4
This commit is contained in:
nf-core-bot
parent
feeb8ba8dd
commit
a560492353
12 changed files with 136 additions and 131 deletions
3
.github/workflows/awsfulltest.yml
vendored
3
.github/workflows/awsfulltest.yml
vendored
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@ -28,6 +28,3 @@ jobs:
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"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/taxprofiler/results-${{ github.sha }}"
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}
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profiles: test_full,aws_tower
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nextflow_config: |
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process.errorStrategy = 'retry'
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process.maxRetries = 3
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3
.github/workflows/awstest.yml
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3
.github/workflows/awstest.yml
vendored
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@ -23,6 +23,3 @@ jobs:
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"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/taxprofiler/results-test-${{ github.sha }}"
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}
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profiles: test,aws_tower
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nextflow_config: |
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process.errorStrategy = 'retry'
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process.maxRetries = 3
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3
.github/workflows/branch.yml
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3
.github/workflows/branch.yml
vendored
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@ -13,7 +13,7 @@ jobs:
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- name: Check PRs
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if: github.repository == 'nf-core/taxprofiler'
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run: |
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"{ [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/taxprofiler ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]"
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{ [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/taxprofiler ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
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# If the above check failed, post a comment on the PR explaining the failure
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# NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
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@ -42,4 +42,3 @@ jobs:
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Thanks again for your contribution!
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repo-token: ${{ secrets.GITHUB_TOKEN }}
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allow-repeats: false
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#
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2
.github/workflows/ci.yml
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2
.github/workflows/ci.yml
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@ -48,5 +48,3 @@ jobs:
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# Remember that you can parallelise this by using strategy.matrix
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run: |
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nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
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#
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55
.github/workflows/fix-linting.yml
vendored
Normal file
55
.github/workflows/fix-linting.yml
vendored
Normal file
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@ -0,0 +1,55 @@
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name: Fix linting from a comment
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on:
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issue_comment:
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types: [created]
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jobs:
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deploy:
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# Only run if comment is on a PR with the main repo, and if it contains the magic keywords
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if: >
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contains(github.event.comment.html_url, '/pull/') &&
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contains(github.event.comment.body, '@nf-core-bot fix linting') &&
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github.repository == 'nf-core/taxprofiler'
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runs-on: ubuntu-latest
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steps:
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# Use the @nf-core-bot token to check out so we can push later
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- uses: actions/checkout@v3
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with:
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token: ${{ secrets.nf_core_bot_auth_token }}
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# Action runs on the issue comment, so we don't get the PR by default
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# Use the gh cli to check out the PR
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- name: Checkout Pull Request
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run: gh pr checkout ${{ github.event.issue.number }}
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env:
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GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
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- uses: actions/setup-node@v2
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- name: Install Prettier
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run: npm install -g prettier @prettier/plugin-php
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# Check that we actually need to fix something
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- name: Run 'prettier --check'
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id: prettier_status
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run: |
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if prettier --check ${GITHUB_WORKSPACE}; then
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echo "::set-output name=result::pass"
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else
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echo "::set-output name=result::fail"
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fi
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- name: Run 'prettier --write'
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if: steps.prettier_status.outputs.result == 'fail'
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run: prettier --write ${GITHUB_WORKSPACE}
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- name: Commit & push changes
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if: steps.prettier_status.outputs.result == 'fail'
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run: |
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git config user.email "core@nf-co.re"
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git config user.name "nf-core-bot"
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git config push.default upstream
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git add .
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git status
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git commit -m "[automated] Fix linting with Prettier"
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git push
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4
.github/workflows/linting.yml
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4
.github/workflows/linting.yml
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@ -48,7 +48,7 @@ jobs:
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wget -qO- get.nextflow.io | bash
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sudo mv nextflow /usr/local/bin/
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- uses: actions/setup-python@v1
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- uses: actions/setup-python@v3
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with:
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python-version: "3.6"
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architecture: "x64"
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@ -78,5 +78,3 @@ jobs:
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lint_log.txt
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lint_results.md
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PR_number.txt
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#
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1
.github/workflows/linting_comment.yml
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1
.github/workflows/linting_comment.yml
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@ -26,4 +26,3 @@ jobs:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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number: ${{ steps.pr_number.outputs.pr_number }}
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path: linting-logs/lint_results.md
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#
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9
.prettierignore
Normal file
9
.prettierignore
Normal file
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@ -0,0 +1,9 @@
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email_template.html
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.nextflow*
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work/
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data/
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results/
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.DS_Store
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testing/
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testing*
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*.pyc
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21
README.md
21
README.md
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@ -1,18 +1,19 @@
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#  
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#  
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[](https://github.com/nf-core/taxprofiler/actions?query=workflow%3A%22nf-core+CI%22)
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[](https://github.com/nf-core/taxprofiler/actions?query=workflow%3A%22nf-core+linting%22)
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[](https://nf-co.re/taxprofiler/results)
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[](https://doi.org/10.5281/zenodo.XXXXXXX)
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[](https://nf-co.re/taxprofiler/results)
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[](https://doi.org/10.5281/zenodo.XXXXXXX)
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[](https://www.nextflow.io/)
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[](https://docs.conda.io/en/latest/)
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[](https://www.docker.com/)
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[](https://sylabs.io/docs/)
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[](https://www.nextflow.io/)
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[](https://docs.conda.io/en/latest/)
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[](https://www.docker.com/)
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[](https://sylabs.io/docs/)
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[](https://tower.nf/launch?pipeline=https://github.com/nf-core/taxprofiler)
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[](https://nfcore.slack.com/channels/taxprofiler)
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[](https://twitter.com/nf_core)
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[](https://www.youtube.com/c/nf-core)
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[](https://nfcore.slack.com/channels/taxprofiler)
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[](https://twitter.com/nf_core)
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[](https://www.youtube.com/c/nf-core)
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## Introduction
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@ -1,111 +1,53 @@
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<html>
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<head>
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<meta charset="utf-8" />
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<meta http-equiv="X-UA-Compatible" content="IE=edge" />
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<meta name="viewport" content="width=device-width, initial-scale=1" />
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<head>
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<meta charset="utf-8">
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<meta http-equiv="X-UA-Compatible" content="IE=edge">
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<meta name="viewport" content="width=device-width, initial-scale=1">
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<!-- prettier-ignore -->
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<meta name="description" content="nf-core/taxprofiler: Taxonomic profiling of shotgun metagenomic data" />
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<title>nf-core/taxprofiler Pipeline Report</title>
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</head>
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<body>
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<div style="font-family: Helvetica, Arial, sans-serif; padding: 30px; max-width: 800px; margin: 0 auto">
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<img src="cid:nfcorepipelinelogo" />
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<meta name="description" content="nf-core/taxprofiler: Taxonomic profiling of shotgun metagenomic data">
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<title>nf-core/taxprofiler Pipeline Report</title>
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</head>
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<body>
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<div style="font-family: Helvetica, Arial, sans-serif; padding: 30px; max-width: 800px; margin: 0 auto;">
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<h1>nf-core/taxprofiler v${version}</h1>
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<h2>Run Name: $runName</h2>
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<img src="cid:nfcorepipelinelogo">
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<% if (!success){ out << """
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<div
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style="
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color: #a94442;
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background-color: #f2dede;
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border-color: #ebccd1;
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padding: 15px;
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margin-bottom: 20px;
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border: 1px solid transparent;
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border-radius: 4px;
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"
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>
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<h4 style="margin-top: 0; color: inherit">nf-core/taxprofiler execution completed unsuccessfully!</h4>
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<h1>nf-core/taxprofiler v${version}</h1>
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<h2>Run Name: $runName</h2>
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<% if (!success){
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out << """
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<div style="color: #a94442; background-color: #f2dede; border-color: #ebccd1; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
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<h4 style="margin-top:0; color: inherit;">nf-core/taxprofiler execution completed unsuccessfully!</h4>
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<p>The exit status of the task that caused the workflow execution to fail was: <code>$exitStatus</code>.</p>
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<p>The full error message was:</p>
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<pre style="white-space: pre-wrap; overflow: visible; margin-bottom: 0">${errorReport}</pre>
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</div>
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""" } else { out << """
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<div
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style="
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color: #3c763d;
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background-color: #dff0d8;
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border-color: #d6e9c6;
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padding: 15px;
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margin-bottom: 20px;
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border: 1px solid transparent;
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border-radius: 4px;
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"
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>
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nf-core/taxprofiler execution completed successfully!
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</div>
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""" } %>
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<p>The workflow was completed at <strong>$dateComplete</strong> (duration: <strong>$duration</strong>)</p>
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<p>The command used to launch the workflow was as follows:</p>
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<pre
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style="
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white-space: pre-wrap;
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overflow: visible;
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background-color: #ededed;
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padding: 15px;
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border-radius: 4px;
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margin-bottom: 30px;
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"
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>
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$commandLine</pre
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>
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<h3>Pipeline Configuration:</h3>
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<table
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style="
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width: 100%;
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max-width: 100%;
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border-spacing: 0;
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border-collapse: collapse;
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border: 0;
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margin-bottom: 30px;
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"
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>
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<tbody style="border-bottom: 1px solid #ddd">
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<% out << summary.collect{ k,v -> "
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<tr>
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<th
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style="
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text-align: left;
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padding: 8px 0;
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line-height: 1.42857143;
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vertical-align: top;
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border-top: 1px solid #ddd;
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"
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>
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$k
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</th>
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<td
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style="
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text-align: left;
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padding: 8px;
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line-height: 1.42857143;
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vertical-align: top;
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border-top: 1px solid #ddd;
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"
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>
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<pre style="white-space: pre-wrap; overflow: visible">$v</pre>
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</td>
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</tr>
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" }.join("\n") %>
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</tbody>
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</table>
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<p>nf-core/taxprofiler</p>
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<p><a href="https://github.com/nf-core/taxprofiler">https://github.com/nf-core/taxprofiler</a></p>
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<pre style="white-space: pre-wrap; overflow: visible; margin-bottom: 0;">${errorReport}</pre>
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</div>
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</body>
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"""
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} else {
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out << """
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<div style="color: #3c763d; background-color: #dff0d8; border-color: #d6e9c6; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
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nf-core/taxprofiler execution completed successfully!
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</div>
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"""
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}
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%>
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<p>The workflow was completed at <strong>$dateComplete</strong> (duration: <strong>$duration</strong>)</p>
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<p>The command used to launch the workflow was as follows:</p>
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<pre style="white-space: pre-wrap; overflow: visible; background-color: #ededed; padding: 15px; border-radius: 4px; margin-bottom:30px;">$commandLine</pre>
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<h3>Pipeline Configuration:</h3>
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<table style="width:100%; max-width:100%; border-spacing: 0; border-collapse: collapse; border:0; margin-bottom: 30px;">
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<tbody style="border-bottom: 1px solid #ddd;">
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<% 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") %>
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</tbody>
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</table>
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<p>nf-core/taxprofiler</p>
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<p><a href="https://github.com/nf-core/taxprofiler">https://github.com/nf-core/taxprofiler</a></p>
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</div>
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</body>
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</html>
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@ -98,7 +98,7 @@ class RowChecker:
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if row[self._first_col] and row[self._second_col]:
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row[self._single_col] = False
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assert (
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Path(row[self._first_col]).suffixes == Path(row[self._second_col]).suffixes
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Path(row[self._first_col]).suffixes[-2:] == Path(row[self._second_col]).suffixes[-2:]
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), "FASTQ pairs must have the same file extensions."
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else:
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row[self._single_col] = True
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@ -129,6 +129,16 @@ class RowChecker:
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row[self._sample_col] = f"{sample}_T{seen[sample]}"
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def read_head(handle, num_lines=10):
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"""Read the specified number of lines from the current position in the file."""
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lines = []
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for idx, line in enumerate(handle):
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if idx == num_lines:
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break
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lines.append(line)
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return "".join(lines)
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def sniff_format(handle):
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"""
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Detect the tabular format.
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@ -144,13 +154,13 @@ def sniff_format(handle):
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https://docs.python.org/3/glossary.html#term-text-file
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"""
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peek = handle.read(2048)
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peek = read_head(handle)
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handle.seek(0)
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sniffer = csv.Sniffer()
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if not sniffer.has_header(peek):
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logger.critical(f"The given sample sheet does not appear to contain a header.")
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sys.exit(1)
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dialect = sniffer.sniff(peek)
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handle.seek(0)
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return dialect
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|
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@ -159,7 +159,7 @@ trace {
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}
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dag {
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enabled = true
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file = "${params.tracedir}/pipeline_dag_${trace_timestamp}.svg"
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file = "${params.tracedir}/pipeline_dag_${trace_timestamp}.html"
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}
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|
||||
manifest {
|
||||
|
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|
|||
Loading…
Reference in a new issue