Merge branch 'dev' into support-aligned-reads
3
.github/workflows/awsfulltest.yml
vendored
|
@ -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
|
|
||||||
|
|
3
.github/workflows/awstest.yml
vendored
|
@ -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
|
|
||||||
|
|
3
.github/workflows/branch.yml
vendored
|
@ -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
|
||||||
#
|
|
||||||
|
|
4
.github/workflows/ci.yml
vendored
|
@ -38,7 +38,7 @@ jobs:
|
||||||
- "--shortread_clipmerge_tool adapterremoval --shortread_clipmerge_mergepairs --shortread_clipmerge_excludeunmerged"
|
- "--shortread_clipmerge_tool adapterremoval --shortread_clipmerge_mergepairs --shortread_clipmerge_excludeunmerged"
|
||||||
- "--shortread_clipmerge_tool adapterremoval --shortread_clipmerge_mergepairs"
|
- "--shortread_clipmerge_tool adapterremoval --shortread_clipmerge_mergepairs"
|
||||||
- "--shortread_complexityfilter_tool bbduk"
|
- "--shortread_complexityfilter_tool bbduk"
|
||||||
- "--shortread_complexityfilter_tool prinseq"
|
- "--shortread_complexityfilter_tool prinseqplusplus"
|
||||||
- "--perform_runmerging"
|
- "--perform_runmerging"
|
||||||
- "--perform_runmerging --shortread_clipmerge_mergepairs"
|
- "--perform_runmerging --shortread_clipmerge_mergepairs"
|
||||||
- "--shortread_complexityfilter false --perform_shortread_hostremoval"
|
- "--shortread_complexityfilter false --perform_shortread_hostremoval"
|
||||||
|
@ -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
|
@ -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
|
4
.github/workflows/linting.yml
vendored
|
@ -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
|
||||||
|
|
||||||
#
|
|
||||||
|
|
1
.github/workflows/linting_comment.yml
vendored
|
@ -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
|
||||||
#
|
|
||||||
|
|
|
@ -1,2 +1,10 @@
|
||||||
|
email_template.html
|
||||||
|
.nextflow*
|
||||||
|
work/
|
||||||
|
data/
|
||||||
|
results/
|
||||||
|
.DS_Store
|
||||||
testing/
|
testing/
|
||||||
|
testing*
|
||||||
tests/
|
tests/
|
||||||
|
*.pyc
|
||||||
|
|
21
README.md
|
@ -1,18 +1,19 @@
|
||||||
# ![nf-core/taxprofiler](docs/images/nf-core-taxprofiler_logo_light.png#gh-light-mode-only) ![nf-core/taxprofiler](docs/images/nf-core-taxprofiler_logo_dark.png#gh-dark-mode-only)
|
# ![nf-core/taxprofiler](docs/images/nf-core-taxprofiler_logo_custom_light.png#gh-light-mode-only) ![nf-core/taxprofiler](docs/images/nf-core-taxprofiler_logo_custom_dark.png#gh-dark-mode-only)
|
||||||
|
|
||||||
[![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
|
||||||
|
|
||||||
|
|
|
@ -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>
|
||||||
|
|
|
@ -9,3 +9,7 @@ report_section_order:
|
||||||
order: -1001
|
order: -1001
|
||||||
|
|
||||||
export_plots: true
|
export_plots: true
|
||||||
|
|
||||||
|
custom_logo: "nf-core-taxprofiler_logo_custom_light.png"
|
||||||
|
custom_logo_url: https://nf-co.re/taxprofiler
|
||||||
|
custom_logo_title: "nf-core/taxprofiler"
|
||||||
|
|
|
@ -54,7 +54,8 @@ process {
|
||||||
params.shortread_clipmerge_skipadaptertrim ? "--disable_adapter_trimming" : "",
|
params.shortread_clipmerge_skipadaptertrim ? "--disable_adapter_trimming" : "",
|
||||||
params.shortread_clipmerge_adapter1 ? "--adapter_sequence ${params.shortread_clipmerge_adapter1}" : "",
|
params.shortread_clipmerge_adapter1 ? "--adapter_sequence ${params.shortread_clipmerge_adapter1}" : "",
|
||||||
// filtering options
|
// filtering options
|
||||||
"--length_required ${params.shortread_clipmerge_minlength}"
|
"--length_required ${params.shortread_clipmerge_minlength}",
|
||||||
|
(params.perform_shortread_complexityfilter && params.shortread_complexityfilter_tool == 'fastp') ? "--low_complexity_filter --complexity_threshold ${params.shortread_complexityfilter_fastp_threshold}" : ''
|
||||||
].join(' ').trim()
|
].join(' ').trim()
|
||||||
ext.prefix = { "${meta.id}_${meta.run_accession}" }
|
ext.prefix = { "${meta.id}_${meta.run_accession}" }
|
||||||
publishDir = [
|
publishDir = [
|
||||||
|
@ -74,7 +75,8 @@ process {
|
||||||
params.shortread_clipmerge_adapter1 ? "--adapter_sequence ${params.shortread_clipmerge_adapter1}" : "",
|
params.shortread_clipmerge_adapter1 ? "--adapter_sequence ${params.shortread_clipmerge_adapter1}" : "",
|
||||||
params.shortread_clipmerge_adapter2 ? "--adapter_sequence_r2 ${params.shortread_clipmerge_adapter2}" : "--detect_adapter_for_pe",
|
params.shortread_clipmerge_adapter2 ? "--adapter_sequence_r2 ${params.shortread_clipmerge_adapter2}" : "--detect_adapter_for_pe",
|
||||||
// filtering options
|
// filtering options
|
||||||
"--length_required ${params.shortread_clipmerge_minlength}"
|
"--length_required ${params.shortread_clipmerge_minlength}",
|
||||||
|
params.perform_shortread_complexityfilter && params.shortread_complexityfilter_tool == 'fastp' ? "--low_complexity_filter --complexity_threshold ${params.shortread_complexityfilter_fastp_threshold}" : ''
|
||||||
].join(' ').trim()
|
].join(' ').trim()
|
||||||
ext.prefix = { "${meta.id}_${meta.run_accession}" }
|
ext.prefix = { "${meta.id}_${meta.run_accession}" }
|
||||||
publishDir = [
|
publishDir = [
|
||||||
|
|
|
@ -29,6 +29,7 @@ params {
|
||||||
perform_shortread_complexityfilter = true
|
perform_shortread_complexityfilter = true
|
||||||
perform_shortread_hostremoval = true
|
perform_shortread_hostremoval = true
|
||||||
perform_longread_hostremoval = true
|
perform_longread_hostremoval = true
|
||||||
|
perform_runmerging = true
|
||||||
hostremoval_reference = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
|
hostremoval_reference = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
|
||||||
run_kaiju = true
|
run_kaiju = true
|
||||||
run_kraken2 = true
|
run_kraken2 = true
|
||||||
|
|
46
conf/test_nopreprocessing.config
Normal file
|
@ -0,0 +1,46 @@
|
||||||
|
/*
|
||||||
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||||
|
Nextflow config file for running minimal tests
|
||||||
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||||
|
Defines input files and everything required to run a fast and simple pipeline test.
|
||||||
|
|
||||||
|
Use as follows:
|
||||||
|
nextflow run nf-core/taxprofiler -profile test,<docker/singularity> --outdir <OUTDIR>
|
||||||
|
|
||||||
|
----------------------------------------------------------------------------------------
|
||||||
|
*/
|
||||||
|
|
||||||
|
params {
|
||||||
|
config_profile_name = 'Test profile'
|
||||||
|
config_profile_description = 'Minimal test dataset skipping all preprocessing to check pipeline function'
|
||||||
|
|
||||||
|
// Limit resources so that this can run on GitHub Actions
|
||||||
|
max_cpus = 2
|
||||||
|
max_memory = '6.GB'
|
||||||
|
max_time = '6.h'
|
||||||
|
|
||||||
|
// Input data
|
||||||
|
// TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
|
||||||
|
// TODO nf-core: Give any required params for the test so that command line flags are not needed
|
||||||
|
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
|
||||||
|
databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
|
||||||
|
perform_shortread_clipmerge = false
|
||||||
|
perform_longread_clip = false
|
||||||
|
perform_shortread_complexityfilter = false
|
||||||
|
perform_shortread_hostremoval = false
|
||||||
|
perform_longread_hostremoval = false
|
||||||
|
perform_runmerging = false
|
||||||
|
hostremoval_reference = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
|
||||||
|
run_kaiju = true
|
||||||
|
run_kraken2 = true
|
||||||
|
run_malt = true
|
||||||
|
run_metaphlan3 = true
|
||||||
|
run_centrifuge = true
|
||||||
|
run_diamond = true
|
||||||
|
}
|
||||||
|
|
||||||
|
process {
|
||||||
|
withName: MALT_RUN {
|
||||||
|
maxForks = 1
|
||||||
|
}
|
||||||
|
}
|
46
conf/test_noprofiling.config
Normal file
|
@ -0,0 +1,46 @@
|
||||||
|
/*
|
||||||
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||||
|
Nextflow config file for running minimal tests
|
||||||
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||||
|
Defines input files and everything required to run a fast and simple pipeline test.
|
||||||
|
|
||||||
|
Use as follows:
|
||||||
|
nextflow run nf-core/taxprofiler -profile test,<docker/singularity> --outdir <OUTDIR>
|
||||||
|
|
||||||
|
----------------------------------------------------------------------------------------
|
||||||
|
*/
|
||||||
|
|
||||||
|
params {
|
||||||
|
config_profile_name = 'Test profile'
|
||||||
|
config_profile_description = 'Minimal test dataset without performing any profiling to check pipeline function'
|
||||||
|
|
||||||
|
// Limit resources so that this can run on GitHub Actions
|
||||||
|
max_cpus = 2
|
||||||
|
max_memory = '6.GB'
|
||||||
|
max_time = '6.h'
|
||||||
|
|
||||||
|
// Input data
|
||||||
|
// TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
|
||||||
|
// TODO nf-core: Give any required params for the test so that command line flags are not needed
|
||||||
|
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
|
||||||
|
databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
|
||||||
|
perform_shortread_clipmerge = true
|
||||||
|
perform_longread_clip = true
|
||||||
|
perform_shortread_complexityfilter = true
|
||||||
|
perform_shortread_hostremoval = true
|
||||||
|
perform_longread_hostremoval = true
|
||||||
|
perform_runmerging = true
|
||||||
|
hostremoval_reference = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
|
||||||
|
run_kaiju = false
|
||||||
|
run_kraken2 = false
|
||||||
|
run_malt = false
|
||||||
|
run_metaphlan3 = false
|
||||||
|
run_centrifuge = false
|
||||||
|
run_diamond = false
|
||||||
|
}
|
||||||
|
|
||||||
|
process {
|
||||||
|
withName: MALT_RUN {
|
||||||
|
maxForks = 1
|
||||||
|
}
|
||||||
|
}
|
BIN
docs/images/nf-core-taxprofiler_icon.png
Normal file
After Width: | Height: | Size: 131 KiB |
444
docs/images/nf-core-taxprofiler_icon.svg
Normal file
|
@ -0,0 +1,444 @@
|
||||||
|
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|
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|
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|
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|
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|
||||||
|
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|
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|
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|
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|
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|
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|
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|
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|
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|
<stop
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|
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|
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|
<stop
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|
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|
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|
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|
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|
||||||
|
</svg>
|
After Width: | Height: | Size: 22 KiB |
BIN
docs/images/nf-core-taxprofiler_logo_custom_dark.png
Normal file
After Width: | Height: | Size: 389 KiB |
2302
docs/images/nf-core-taxprofiler_logo_custom_dark.svg
Normal file
After Width: | Height: | Size: 87 KiB |
BIN
docs/images/nf-core-taxprofiler_logo_custom_light.png
Normal file
After Width: | Height: | Size: 433 KiB |
2305
docs/images/nf-core-taxprofiler_logo_custom_light.svg
Normal file
After Width: | Height: | Size: 87 KiB |
3223
docs/images/taxprofiler_logo.svg
Normal file
After Width: | Height: | Size: 124 KiB |
|
@ -183,11 +183,11 @@ Complexity filtering can be activated via the `--perform_shortread_complexityfil
|
||||||
|
|
||||||
Complexity filtering is primarily a run-time optimisation step. It is not necessary for accurate taxonomic profiling, however it can speed up run-time of each tool by removing reads with low-diversity of nucleotides (e.g. with mono-nucleotide - `AAAAAAAA`, or di-nucleotide repeats `GAGAGAGAGAGAGAG`) that have a low-chance of giving an informative taxonomic ID as they can be associated with many different taxa. Removing these reads therefore saves computational time and resources.
|
Complexity filtering is primarily a run-time optimisation step. It is not necessary for accurate taxonomic profiling, however it can speed up run-time of each tool by removing reads with low-diversity of nucleotides (e.g. with mono-nucleotide - `AAAAAAAA`, or di-nucleotide repeats `GAGAGAGAGAGAGAG`) that have a low-chance of giving an informative taxonomic ID as they can be associated with many different taxa. Removing these reads therefore saves computational time and resources.
|
||||||
|
|
||||||
There are currently two options for short-read complexity filtering: [`bbduk`](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/) and [`prinseq++`](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/).
|
There are currently three options for short-read complexity filtering: [`bbduk`](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/), [`prinseq++`](https://github.com/Adrian-Cantu/PRINSEQ-plus-plus), and [`fastp`](https://github.com/OpenGene/fastp#low-complexity-filter).
|
||||||
|
|
||||||
The tools offer different algorithms and parameters for removing low complexity reads. We therefore recommend reviewing the pipeline's [parameter documentation](https://nf-co.re/taxprofiler/parameters) and the documentation of both tools (see links above) to decide on optimal methods and parameters for your dataset.
|
The tools offer different algorithms and parameters for removing low complexity reads. We therefore recommend reviewing the pipeline's [parameter documentation](https://nf-co.re/taxprofiler/parameters) and the documentation of the tools (see links above) to decide on optimal methods and parameters for your dataset.
|
||||||
|
|
||||||
You can optionally save the FASTQ output of the run merging with the `--save_complexityfiltered_reads`.
|
You can optionally save the FASTQ output of the run merging with the `--save_complexityfiltered_reads`. If running with `fastp`, complexity filtering happens inclusively within the earlier shortread preprocessing step. Therefore there will not be an independent pipeline step for complexity filtering, and no independent FASTQ file (i.e. `--save_complexityfiltered_reads` will be ignored) - your complexity filtered reads will also be in the `fastp/` folder in the same file(s) as the preprocessed read.
|
||||||
|
|
||||||
#### Host Removal
|
#### Host Removal
|
||||||
|
|
||||||
|
|
|
@ -74,6 +74,7 @@ params {
|
||||||
shortread_complexityfilter_bbduk_mask = false
|
shortread_complexityfilter_bbduk_mask = false
|
||||||
shortread_complexityfilter_prinseqplusplus_mode = 'entropy'
|
shortread_complexityfilter_prinseqplusplus_mode = 'entropy'
|
||||||
shortread_complexityfilter_prinseqplusplus_dustscore = 0.5
|
shortread_complexityfilter_prinseqplusplus_dustscore = 0.5
|
||||||
|
shortread_complexityfilter_fastp_threshold = 30
|
||||||
save_complexityfiltered_reads = false
|
save_complexityfiltered_reads = false
|
||||||
|
|
||||||
// run merging
|
// run merging
|
||||||
|
@ -131,11 +132,11 @@ try {
|
||||||
|
|
||||||
// Load nf-core/taxprofiler custom profiles from different institutions.
|
// Load nf-core/taxprofiler custom profiles from different institutions.
|
||||||
// Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs!
|
// Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs!
|
||||||
// try {
|
try {
|
||||||
// includeConfig "${params.custom_config_base}/pipeline/taxprofiler.config"
|
includeConfig "${params.custom_config_base}/pipeline/taxprofiler.config"
|
||||||
// } catch (Exception e) {
|
} catch (Exception e) {
|
||||||
// System.err.println("WARNING: Could not load nf-core/config/taxprofiler profiles: ${params.custom_config_base}/pipeline/taxprofiler.config")
|
System.err.println("WARNING: Could not load nf-core/config/taxprofiler profiles: ${params.custom_config_base}/pipeline/taxprofiler.config")
|
||||||
// }
|
}
|
||||||
|
|
||||||
|
|
||||||
profiles {
|
profiles {
|
||||||
|
@ -187,6 +188,8 @@ profiles {
|
||||||
}
|
}
|
||||||
test { includeConfig 'conf/test.config' }
|
test { includeConfig 'conf/test.config' }
|
||||||
test_full { includeConfig 'conf/test_full.config' }
|
test_full { includeConfig 'conf/test_full.config' }
|
||||||
|
test_noprofiling { includeConfig 'conf/test_noprofiling.config' }
|
||||||
|
test_nopreprocessing { includeConfig 'conf/test_preprocessing.config' }
|
||||||
}
|
}
|
||||||
|
|
||||||
// Load igenomes.config if required
|
// Load igenomes.config if required
|
||||||
|
@ -225,7 +228,7 @@ trace {
|
||||||
}
|
}
|
||||||
dag {
|
dag {
|
||||||
enabled = true
|
enabled = true
|
||||||
file = "${params.tracedir}/pipeline_dag_${trace_timestamp}.svg"
|
file = "${params.tracedir}/pipeline_dag_${trace_timestamp}.html"
|
||||||
}
|
}
|
||||||
|
|
||||||
manifest {
|
manifest {
|
||||||
|
|
|
@ -323,7 +323,8 @@
|
||||||
},
|
},
|
||||||
"shortread_complexityfilter_tool": {
|
"shortread_complexityfilter_tool": {
|
||||||
"type": "string",
|
"type": "string",
|
||||||
"default": "bbduk"
|
"default": "bbduk",
|
||||||
|
"enum": ["bbduk", "prinseqplusplus", "fastp"]
|
||||||
},
|
},
|
||||||
"shortread_complexityfilter_bbduk_windowsize": {
|
"shortread_complexityfilter_bbduk_windowsize": {
|
||||||
"type": "integer",
|
"type": "integer",
|
||||||
|
@ -427,6 +428,10 @@
|
||||||
"type": "string",
|
"type": "string",
|
||||||
"default": "None"
|
"default": "None"
|
||||||
},
|
},
|
||||||
|
"shortread_complexityfilter_fastp_threshold": {
|
||||||
|
"type": "integer",
|
||||||
|
"default": 30
|
||||||
|
},
|
||||||
"malt_save_reads": {
|
"malt_save_reads": {
|
||||||
"type": "boolean"
|
"type": "boolean"
|
||||||
},
|
},
|
||||||
|
|
|
@ -13,6 +13,7 @@ workflow SHORTREAD_COMPLEXITYFILTERING {
|
||||||
ch_versions = Channel.empty()
|
ch_versions = Channel.empty()
|
||||||
ch_multiqc_files = Channel.empty()
|
ch_multiqc_files = Channel.empty()
|
||||||
|
|
||||||
|
// fastp complexity filtering is activated via modules.conf in shortread_preprocessing
|
||||||
if ( params.shortread_complexityfilter_tool == 'bbduk' ) {
|
if ( params.shortread_complexityfilter_tool == 'bbduk' ) {
|
||||||
ch_filtered_reads = BBMAP_BBDUK ( reads, [] ).reads
|
ch_filtered_reads = BBMAP_BBDUK ( reads, [] ).reads
|
||||||
ch_versions = ch_versions.mix( BBMAP_BBDUK.out.versions.first() )
|
ch_versions = ch_versions.mix( BBMAP_BBDUK.out.versions.first() )
|
||||||
|
|
|
@ -19,9 +19,12 @@ for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true
|
||||||
// Check mandatory parameters
|
// Check mandatory parameters
|
||||||
if (params.input ) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' }
|
if (params.input ) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' }
|
||||||
if (params.databases) { ch_databases = file(params.databases) } else { exit 1, 'Input database sheet not specified!' }
|
if (params.databases) { ch_databases = file(params.databases) } else { exit 1, 'Input database sheet not specified!' }
|
||||||
|
|
||||||
if (params.shortread_clipmerge_mergepairs && params.run_malt ) log.warn "[nf-core/taxprofiler] MALT does not accept uncollapsed paired-reads. Pairs will be profiled as separate files."
|
if (params.shortread_clipmerge_mergepairs && params.run_malt ) log.warn "[nf-core/taxprofiler] MALT does not accept uncollapsed paired-reads. Pairs will be profiled as separate files."
|
||||||
if (params.shortread_clipmerge_excludeunmerged && !params.shortread_clipmerge_mergepairs) exit 1, "ERROR: [nf-core/taxprofiler] cannot include unmerged reads when merging not turned on. Please specify --shortread_clipmerge_mergepairs"
|
if (params.shortread_clipmerge_excludeunmerged && !params.shortread_clipmerge_mergepairs) exit 1, "ERROR: [nf-core/taxprofiler] cannot include unmerged reads when merging not turned on. Please specify --shortread_clipmerge_mergepairs"
|
||||||
|
|
||||||
|
if (params.shortread_complexityfilter_tool == 'fastp' && ( params.perform_shortread_clipmerge == false || params.shortread_clipmerge_tool != 'fastp' )) exit 1, "ERROR: [nf-core/taxprofiler] cannot use fastp complexity filtering if preprocessing not turned on and/or tool is not fastp. Please specify --perform_shortread_clipmerge and/or --shortread_clipmerge_tool 'fastp'"
|
||||||
|
|
||||||
if (params.perform_shortread_hostremoval && !params.hostremoval_reference) { exit 1, "ERROR: [nf-core/taxprofiler] --shortread_hostremoval requested but no --hostremoval_reference FASTA supplied. Check input." }
|
if (params.perform_shortread_hostremoval && !params.hostremoval_reference) { exit 1, "ERROR: [nf-core/taxprofiler] --shortread_hostremoval requested but no --hostremoval_reference FASTA supplied. Check input." }
|
||||||
if (!params.hostremoval_reference && params.hostremoval_reference_index) { exit 1, "ERROR: [nf-core/taxprofiler] --shortread_hostremoval_index provided but no --hostremoval_reference FASTA supplied. Check input." }
|
if (!params.hostremoval_reference && params.hostremoval_reference_index) { exit 1, "ERROR: [nf-core/taxprofiler] --shortread_hostremoval_index provided but no --hostremoval_reference FASTA supplied. Check input." }
|
||||||
|
|
||||||
|
@ -86,6 +89,7 @@ def multiqc_report = []
|
||||||
workflow TAXPROFILER {
|
workflow TAXPROFILER {
|
||||||
|
|
||||||
ch_versions = Channel.empty()
|
ch_versions = Channel.empty()
|
||||||
|
ch_taxprofiler_logo = Channel.fromPath("$projectDir/docs/images/nf-core-taxprofiler_logo_custom_light.png")
|
||||||
|
|
||||||
/*
|
/*
|
||||||
SUBWORKFLOW: Read in samplesheet, validate and stage input files
|
SUBWORKFLOW: Read in samplesheet, validate and stage input files
|
||||||
|
@ -133,7 +137,8 @@ workflow TAXPROFILER {
|
||||||
SUBWORKFLOW: COMPLEXITY FILTERING
|
SUBWORKFLOW: COMPLEXITY FILTERING
|
||||||
*/
|
*/
|
||||||
|
|
||||||
if ( params.perform_shortread_complexityfilter ) {
|
// fastp complexity filtering is activated via modules.conf in shortread_preprocessing
|
||||||
|
if ( params.perform_shortread_complexityfilter && params.shortread_complexityfilter_tool != 'fastp' ) {
|
||||||
ch_shortreads_filtered = SHORTREAD_COMPLEXITYFILTERING ( ch_shortreads_preprocessed ).reads
|
ch_shortreads_filtered = SHORTREAD_COMPLEXITYFILTERING ( ch_shortreads_preprocessed ).reads
|
||||||
ch_versions = ch_versions.mix( SHORTREAD_COMPLEXITYFILTERING.out.versions )
|
ch_versions = ch_versions.mix( SHORTREAD_COMPLEXITYFILTERING.out.versions )
|
||||||
} else {
|
} else {
|
||||||
|
@ -222,6 +227,8 @@ workflow TAXPROFILER {
|
||||||
ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
|
ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
|
||||||
ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
|
ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
|
||||||
|
|
||||||
|
ch_multiqc_files = ch_multiqc_files.mix(ch_taxprofiler_logo.ifEmpty([]))
|
||||||
|
|
||||||
if (params.perform_shortread_clipmerge) {
|
if (params.perform_shortread_clipmerge) {
|
||||||
ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) )
|
ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) )
|
||||||
}
|
}
|
||||||
|
@ -230,7 +237,7 @@ workflow TAXPROFILER {
|
||||||
ch_multiqc_files = ch_multiqc_files.mix( LONGREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) )
|
ch_multiqc_files = ch_multiqc_files.mix( LONGREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) )
|
||||||
}
|
}
|
||||||
|
|
||||||
if (params.perform_shortread_complexityfilter){
|
if (params.perform_shortread_complexityfilter && params.shortread_complexityfilter_tool != 'fastp'){
|
||||||
ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_COMPLEXITYFILTERING.out.mqc.collect{it[1]}.ifEmpty([]) )
|
ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_COMPLEXITYFILTERING.out.mqc.collect{it[1]}.ifEmpty([]) )
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|