millironx/taxprofiler
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Merge branch 'dev' into support-aligned-reads

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James A. Fellows Yates 2022-06-02 12:45:29 +02:00 committed by GitHub
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27 changed files with 8525 additions and 142 deletions
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3
.github/workflows/awsfulltest.yml vendored
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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

3
.github/workflows/awstest.yml vendored
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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

3
.github/workflows/branch.yml vendored
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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
#

4
.github/workflows/ci.yml vendored
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@ -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
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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

4
.github/workflows/linting.yml vendored
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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
#

1
.github/workflows/linting_comment.yml vendored
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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
#

8
.prettierignore
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@ -1,2 +1,10 @@
email_template.html
.nextflow*
work/
data/
results/
.DS_Store
testing/ testing/
testing*
tests/ tests/
*.pyc

21
README.md
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@ -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

108
assets/email_template.html
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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>

4
assets/multiqc_config.yml
View file

@ -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"

6
conf/modules.config
View file

@ -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 = [

1
conf/test.config
View file

@ -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
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@ -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
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@ -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
}
}

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<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!-- Created with Inkscape (http://www.inkscape.org/) -->
<svg
width="160mm"
height="120mm"
viewBox="0 0 160 120"
version="1.1"
id="svg5581"
inkscape:version="1.2 (1:1.2+202205241504+da316b6974)"
sodipodi:docname="nf-core-taxprofiler_icon.svg"
xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
xmlns:xlink="http://www.w3.org/1999/xlink"
xmlns="http://www.w3.org/2000/svg"
xmlns:svg="http://www.w3.org/2000/svg">
<sodipodi:namedview
id="namedview5583"
pagecolor="#ffffff"
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6
docs/usage.md
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@ -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

15
nextflow.config
View file

@ -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 {

7
nextflow_schema.json
View file

@ -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"
}, },

1
subworkflows/local/shortread_complexityfiltering.nf
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@ -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() )

11
workflows/taxprofiler.nf
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@ -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([]) )
} }