mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-13 07:03:10 +00:00
Merge branch 'dev' of github.com:nf-core/taxprofiler into add-filtlong
This commit is contained in:
commit
310ac6b450
31 changed files with 859 additions and 233 deletions
3
.github/workflows/awsfulltest.yml
vendored
3
.github/workflows/awsfulltest.yml
vendored
|
@ -28,6 +28,3 @@ jobs:
|
|||
"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/taxprofiler/results-${{ github.sha }}"
|
||||
}
|
||||
profiles: test_full,aws_tower
|
||||
nextflow_config: |
|
||||
process.errorStrategy = 'retry'
|
||||
process.maxRetries = 3
|
||||
|
|
3
.github/workflows/awstest.yml
vendored
3
.github/workflows/awstest.yml
vendored
|
@ -23,6 +23,3 @@ jobs:
|
|||
"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/taxprofiler/results-test-${{ github.sha }}"
|
||||
}
|
||||
profiles: test,aws_tower
|
||||
nextflow_config: |
|
||||
process.errorStrategy = 'retry'
|
||||
process.maxRetries = 3
|
||||
|
|
3
.github/workflows/branch.yml
vendored
3
.github/workflows/branch.yml
vendored
|
@ -13,7 +13,7 @@ jobs:
|
|||
- name: Check PRs
|
||||
if: github.repository == 'nf-core/taxprofiler'
|
||||
run: |
|
||||
"{ [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/taxprofiler ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]"
|
||||
{ [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/taxprofiler ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
|
||||
|
||||
# If the above check failed, post a comment on the PR explaining the failure
|
||||
# NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
|
||||
|
@ -42,4 +42,3 @@ jobs:
|
|||
Thanks again for your contribution!
|
||||
repo-token: ${{ secrets.GITHUB_TOKEN }}
|
||||
allow-repeats: false
|
||||
#
|
||||
|
|
4
.github/workflows/ci.yml
vendored
4
.github/workflows/ci.yml
vendored
|
@ -38,7 +38,7 @@ jobs:
|
|||
- "--shortread_qc_tool adapterremoval --shortread_qc_mergepairs --shortread_qc_excludeunmerged"
|
||||
- "--shortread_qc_tool adapterremoval --shortread_qc_mergepairs"
|
||||
- "--shortread_complexityfilter_tool bbduk"
|
||||
- "--shortread_complexityfilter_tool prinseq"
|
||||
- "--shortread_complexityfilter_tool prinseqplusplus"
|
||||
- "--perform_runmerging"
|
||||
- "--perform_runmerging --shortread_qc_mergepairs"
|
||||
- "--shortread_complexityfilter false --perform_shortread_hostremoval"
|
||||
|
@ -71,5 +71,3 @@ jobs:
|
|||
# Remember that you can parallelise this by using strategy.matrix
|
||||
run: |
|
||||
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }}
|
||||
|
||||
#
|
||||
|
|
55
.github/workflows/fix-linting.yml
vendored
Normal file
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
4
.github/workflows/linting.yml
vendored
|
@ -48,7 +48,7 @@ jobs:
|
|||
wget -qO- get.nextflow.io | bash
|
||||
sudo mv nextflow /usr/local/bin/
|
||||
|
||||
- uses: actions/setup-python@v1
|
||||
- uses: actions/setup-python@v3
|
||||
with:
|
||||
python-version: "3.6"
|
||||
architecture: "x64"
|
||||
|
@ -78,5 +78,3 @@ jobs:
|
|||
lint_log.txt
|
||||
lint_results.md
|
||||
PR_number.txt
|
||||
|
||||
#
|
||||
|
|
1
.github/workflows/linting_comment.yml
vendored
1
.github/workflows/linting_comment.yml
vendored
|
@ -26,4 +26,3 @@ jobs:
|
|||
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
|
||||
number: ${{ steps.pr_number.outputs.pr_number }}
|
||||
path: linting-logs/lint_results.md
|
||||
#
|
||||
|
|
|
@ -1,2 +1,10 @@
|
|||
email_template.html
|
||||
.nextflow*
|
||||
work/
|
||||
data/
|
||||
results/
|
||||
.DS_Store
|
||||
testing/
|
||||
testing*
|
||||
tests/
|
||||
*.pyc
|
||||
|
|
19
README.md
19
README.md
|
@ -2,17 +2,18 @@
|
|||
|
||||
[![GitHub Actions CI Status](https://github.com/nf-core/taxprofiler/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/taxprofiler/actions?query=workflow%3A%22nf-core+CI%22)
|
||||
[![GitHub Actions Linting Status](https://github.com/nf-core/taxprofiler/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/taxprofiler/actions?query=workflow%3A%22nf-core+linting%22)
|
||||
[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/taxprofiler/results)
|
||||
[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
|
||||
[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?logo=Amazon%20AWS)](https://nf-co.re/taxprofiler/results)
|
||||
[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8)](https://doi.org/10.5281/zenodo.XXXXXXX)
|
||||
|
||||
[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg?labelColor=000000)](https://www.nextflow.io/)
|
||||
[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
|
||||
[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
|
||||
[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
|
||||
[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg)](https://www.nextflow.io/)
|
||||
[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?logo=anaconda)](https://docs.conda.io/en/latest/)
|
||||
[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?logo=docker)](https://www.docker.com/)
|
||||
[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg)](https://sylabs.io/docs/)
|
||||
[![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/taxprofiler)
|
||||
|
||||
[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23taxprofiler-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/taxprofiler)
|
||||
[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)
|
||||
[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)
|
||||
[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23taxprofiler-4A154B?logo=slack)](https://nfcore.slack.com/channels/taxprofiler)
|
||||
[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?logo=twitter)](https://twitter.com/nf_core)
|
||||
[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?logo=youtube)](https://www.youtube.com/c/nf-core)
|
||||
|
||||
## Introduction
|
||||
|
||||
|
|
|
@ -1,111 +1,53 @@
|
|||
<html>
|
||||
<head>
|
||||
<meta charset="utf-8" />
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge" />
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1" />
|
||||
<head>
|
||||
<meta charset="utf-8">
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<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" />
|
||||
<title>nf-core/taxprofiler Pipeline Report</title>
|
||||
</head>
|
||||
<body>
|
||||
<div style="font-family: Helvetica, Arial, sans-serif; padding: 30px; max-width: 800px; margin: 0 auto">
|
||||
<img src="cid:nfcorepipelinelogo" />
|
||||
<meta name="description" content="nf-core/taxprofiler: Taxonomic profiling of shotgun metagenomic data">
|
||||
<title>nf-core/taxprofiler Pipeline Report</title>
|
||||
</head>
|
||||
<body>
|
||||
<div style="font-family: Helvetica, Arial, sans-serif; padding: 30px; max-width: 800px; margin: 0 auto;">
|
||||
|
||||
<h1>nf-core/taxprofiler v${version}</h1>
|
||||
<h2>Run Name: $runName</h2>
|
||||
<img src="cid:nfcorepipelinelogo">
|
||||
|
||||
<% if (!success){ out << """
|
||||
<div
|
||||
style="
|
||||
color: #a94442;
|
||||
background-color: #f2dede;
|
||||
border-color: #ebccd1;
|
||||
padding: 15px;
|
||||
margin-bottom: 20px;
|
||||
border: 1px solid transparent;
|
||||
border-radius: 4px;
|
||||
"
|
||||
>
|
||||
<h4 style="margin-top: 0; color: inherit">nf-core/taxprofiler execution completed unsuccessfully!</h4>
|
||||
<h1>nf-core/taxprofiler v${version}</h1>
|
||||
<h2>Run Name: $runName</h2>
|
||||
|
||||
<% if (!success){
|
||||
out << """
|
||||
<div style="color: #a94442; background-color: #f2dede; border-color: #ebccd1; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
|
||||
<h4 style="margin-top:0; color: inherit;">nf-core/taxprofiler execution completed unsuccessfully!</h4>
|
||||
<p>The exit status of the task that caused the workflow execution to fail was: <code>$exitStatus</code>.</p>
|
||||
<p>The full error message was:</p>
|
||||
<pre style="white-space: pre-wrap; overflow: visible; margin-bottom: 0">${errorReport}</pre>
|
||||
</div>
|
||||
""" } else { out << """
|
||||
<div
|
||||
style="
|
||||
color: #3c763d;
|
||||
background-color: #dff0d8;
|
||||
border-color: #d6e9c6;
|
||||
padding: 15px;
|
||||
margin-bottom: 20px;
|
||||
border: 1px solid transparent;
|
||||
border-radius: 4px;
|
||||
"
|
||||
>
|
||||
nf-core/taxprofiler execution completed successfully!
|
||||
</div>
|
||||
""" } %>
|
||||
|
||||
<p>The workflow was completed at <strong>$dateComplete</strong> (duration: <strong>$duration</strong>)</p>
|
||||
<p>The command used to launch the workflow was as follows:</p>
|
||||
<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>
|
||||
<table
|
||||
style="
|
||||
width: 100%;
|
||||
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>
|
||||
</table>
|
||||
|
||||
<p>nf-core/taxprofiler</p>
|
||||
<p><a href="https://github.com/nf-core/taxprofiler">https://github.com/nf-core/taxprofiler</a></p>
|
||||
<pre style="white-space: pre-wrap; overflow: visible; margin-bottom: 0;">${errorReport}</pre>
|
||||
</div>
|
||||
</body>
|
||||
"""
|
||||
} else {
|
||||
out << """
|
||||
<div style="color: #3c763d; background-color: #dff0d8; border-color: #d6e9c6; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
|
||||
nf-core/taxprofiler execution completed successfully!
|
||||
</div>
|
||||
"""
|
||||
}
|
||||
%>
|
||||
|
||||
<p>The workflow was completed at <strong>$dateComplete</strong> (duration: <strong>$duration</strong>)</p>
|
||||
<p>The command used to launch the workflow was as follows:</p>
|
||||
<pre style="white-space: pre-wrap; overflow: visible; background-color: #ededed; padding: 15px; border-radius: 4px; margin-bottom:30px;">$commandLine</pre>
|
||||
|
||||
<h3>Pipeline Configuration:</h3>
|
||||
<table style="width:100%; 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>
|
||||
</table>
|
||||
|
||||
<p>nf-core/taxprofiler</p>
|
||||
<p><a href="https://github.com/nf-core/taxprofiler">https://github.com/nf-core/taxprofiler</a></p>
|
||||
|
||||
</div>
|
||||
|
||||
</body>
|
||||
</html>
|
||||
|
|
|
@ -54,7 +54,8 @@ process {
|
|||
params.shortread_qc_skipadaptertrim ? "--disable_adapter_trimming" : "",
|
||||
params.shortread_qc_adapter1 ? "--adapter_sequence ${params.shortread_qc_adapter1}" : "",
|
||||
// filtering options
|
||||
"--length_required ${params.shortread_qc_minlength}"
|
||||
"--length_required ${params.shortread_clipmerge_minlength}",
|
||||
(params.perform_shortread_complexityfilter && params.shortread_complexityfilter_tool == 'fastp') ? "--low_complexity_filter --complexity_threshold ${params.shortread_complexityfilter_fastp_threshold}" : ''
|
||||
].join(' ').trim()
|
||||
ext.prefix = { "${meta.id}_${meta.run_accession}" }
|
||||
publishDir = [
|
||||
|
@ -74,7 +75,8 @@ process {
|
|||
params.shortread_qc_adapter1 ? "--adapter_sequence ${params.shortread_qc_adapter1}" : "",
|
||||
params.shortread_qc_adapter2 ? "--adapter_sequence_r2 ${params.shortread_qc_adapter2}" : "--detect_adapter_for_pe",
|
||||
// filtering options
|
||||
"--length_required ${params.shortread_qc_minlength}"
|
||||
"--length_required ${params.shortread_clipmerge_minlength}",
|
||||
params.perform_shortread_complexityfilter && params.shortread_complexityfilter_tool == 'fastp' ? "--low_complexity_filter --complexity_threshold ${params.shortread_complexityfilter_fastp_threshold}" : ''
|
||||
].join(' ').trim()
|
||||
ext.prefix = { "${meta.id}_${meta.run_accession}" }
|
||||
publishDir = [
|
||||
|
@ -180,6 +182,47 @@ process {
|
|||
]
|
||||
}
|
||||
|
||||
withName: MINIMAP2_INDEX {
|
||||
ext.args = '-x map-ont'
|
||||
publishDir = [
|
||||
path: { "${params.outdir}/minimap2/index" },
|
||||
mode: params.publish_dir_mode,
|
||||
enabled: params.save_hostremoval_index,
|
||||
pattern: 'minimap2'
|
||||
]
|
||||
}
|
||||
|
||||
withName: MINIMAP2_ALIGN {
|
||||
ext.prefix = { "${meta.id}_${meta.run_accession}" }
|
||||
publishDir = [
|
||||
path: { "${params.outdir}/minimap2/align" },
|
||||
mode: params.publish_dir_mode,
|
||||
enabled: params.save_hostremoval_mapped,
|
||||
pattern: '*.bam'
|
||||
]
|
||||
}
|
||||
|
||||
withName: SAMTOOLS_VIEW {
|
||||
ext.args = '-f 4'
|
||||
ext.prefix = { "${meta.id}.mapped.sorted" }
|
||||
publishDir = [
|
||||
path: { "${params.outdir}/samtools/view" },
|
||||
mode: params.publish_dir_mode,
|
||||
enabled: params.save_hostremoval_unmapped,
|
||||
pattern: '*.bam'
|
||||
]
|
||||
}
|
||||
|
||||
withName: SAMTOOLS_BAM2FQ {
|
||||
ext.prefix = { "${meta.id}_${meta.run_accession}" }
|
||||
publishDir = [
|
||||
path: { "${params.outdir}/samtools/bam2fq" },
|
||||
mode: params.publish_dir_mode,
|
||||
enabled: params.save_hostremoval_unmapped,
|
||||
pattern: '*.fq.gz'
|
||||
]
|
||||
}
|
||||
|
||||
withName: BBMAP_BBDUK {
|
||||
ext.args = [
|
||||
"entropy=${params.shortread_complexityfilter_entropy}",
|
||||
|
|
|
@ -28,7 +28,9 @@ params {
|
|||
perform_longread_qc = false
|
||||
perform_shortread_complexityfilter = true
|
||||
perform_shortread_hostremoval = true
|
||||
shortread_hostremoval_reference = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
|
||||
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 = true
|
||||
run_kraken2 = true
|
||||
run_malt = true
|
||||
|
|
46
conf/test_nopreprocessing.config
Normal file
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
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
|
||||
}
|
||||
}
|
|
@ -183,21 +183,21 @@ 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.
|
||||
|
||||
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
|
||||
|
||||
Removal of possible-host reads from FASTQ files prior profiling can be activated with `--perform_shortread_hostremoval`
|
||||
Removal of possible-host reads from FASTQ files prior profiling can be activated with `--perform_shortread_hostremoval` or `--perform_longread_hostremoval`.
|
||||
|
||||
Similarly to complexity filtering, host-removal can be useful for runtime optimisation and reduction in misclassified reads. It is not always necessary to report classification of reads from a host when you already know the host of the sample, therefore you can gain a run-time and computational advantage by removing these prior typically resource-heavy profiling with more efficient methods. Furthermore, particularly with human samples, you can reduce the number of false positives during profiling that occur due to host-sequence contamination in reference genomes on public databases.
|
||||
|
||||
nf-core/taxprofiler currently offers host-removal via alignment against a reference genome with Bowtie2, and the use of the unaligned reads for downstream profiling.
|
||||
|
||||
You can supply your reference genome in FASTA format with `--shortread_hostremoval_reference`. You can also optionally supply a directory containing pre-indexed Bowtie2 index files with `--shortread_hostremoval_index`, however nf-core/taxprofiler will generate this for you if necessary. Pre-supplying the directory of index files can greatly speed up the process, and these can be re-used.
|
||||
You can supply your reference genome in FASTA format with `--hostremoval_reference`. You can also optionally supply a directory containing pre-indexed Bowtie2 index files with `--shortread_hostremoval_index` or `--longread_hostremoval_index`, however nf-core/taxprofiler will generate this for you if necessary. Pre-supplying the directory of index files can greatly speed up the process, and these can be re-used.
|
||||
|
||||
> 💡 If you have multiple taxa or sequences you wish to remove (e.g., the host genome and then also PhiX - common quality-control reagent during sequencing) you can simply concatenate the FASTAs of each taxa or sequences into a single reference file.
|
||||
|
||||
|
|
12
modules.json
12
modules.json
|
@ -55,6 +55,12 @@
|
|||
"git_sha": "2d38566eca4cc15142b2ffa7c11837569b39aece"
|
||||
},
|
||||
"metaphlan3": {
|
||||
"git_sha": "ed4dd1a928ebf4308efb720de878045f7773f8e2"
|
||||
},
|
||||
"minimap2/align": {
|
||||
"git_sha": "1a5a9e7b4009dcf34e6867dd1a5a1d9a718b027b"
|
||||
},
|
||||
"minimap2/index": {
|
||||
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
|
||||
},
|
||||
"multiqc": {
|
||||
|
@ -66,6 +72,12 @@
|
|||
"prinseqplusplus": {
|
||||
"git_sha": "f1c5384c31e985591716afdd732cf8c2ae29d05b"
|
||||
},
|
||||
"samtools/bam2fq": {
|
||||
"git_sha": "5510ea39fe638594bc26ac34cadf4a84bf27d159"
|
||||
},
|
||||
"samtools/view": {
|
||||
"git_sha": "6b64f9cb6c3dd3577931cc3cd032d6fb730000ce"
|
||||
},
|
||||
"untar": {
|
||||
"git_sha": "e080f4c8acf5760039ed12ec1f206170f3f9a918"
|
||||
}
|
||||
|
|
2
modules/nf-core/modules/metaphlan3/main.nf
generated
2
modules/nf-core/modules/metaphlan3/main.nf
generated
|
@ -23,7 +23,7 @@ process METAPHLAN3 {
|
|||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
def input_type = ("$input".endsWith(".fastq.gz")) ? "--input_type fastq" : ("$input".contains(".fasta")) ? "--input_type fasta" : ("$input".endsWith(".bowtie2out.txt")) ? "--input_type bowtie2out" : "--input_type sam"
|
||||
def input_type = ("$input".endsWith(".fastq.gz") || "$input".endsWith(".fq.gz")) ? "--input_type fastq" : ("$input".contains(".fasta")) ? "--input_type fasta" : ("$input".endsWith(".bowtie2out.txt")) ? "--input_type bowtie2out" : "--input_type sam"
|
||||
def input_data = ("$input_type".contains("fastq")) && !meta.single_end ? "${input[0]},${input[1]}" : "$input"
|
||||
def bowtie2_out = "$input_type" == "--input_type bowtie2out" || "$input_type" == "--input_type sam" ? '' : "--bowtie2out ${prefix}.bowtie2out.txt"
|
||||
|
||||
|
|
48
modules/nf-core/modules/minimap2/align/main.nf
generated
Normal file
48
modules/nf-core/modules/minimap2/align/main.nf
generated
Normal file
|
@ -0,0 +1,48 @@
|
|||
process MINIMAP2_ALIGN {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? 'bioconda::minimap2=2.21 bioconda::samtools=1.12' : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0' :
|
||||
'quay.io/biocontainers/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(reads)
|
||||
path reference
|
||||
val bam_format
|
||||
val cigar_paf_format
|
||||
val cigar_bam
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.paf"), optional: true, emit: paf
|
||||
tuple val(meta), path("*.bam"), optional: true, emit: bam
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
def input_reads = meta.single_end ? "$reads" : "${reads[0]} ${reads[1]}"
|
||||
def bam_output = bam_format ? "-a | samtools sort | samtools view -@ ${task.cpus} -b -h -o ${prefix}.bam" : "-o ${prefix}.paf"
|
||||
def cigar_paf = cigar_paf_format && !bam_format ? "-c" : ''
|
||||
def set_cigar_bam = cigar_bam && bam_format ? "-L" : ''
|
||||
"""
|
||||
minimap2 \\
|
||||
$args \\
|
||||
-t $task.cpus \\
|
||||
$reference \\
|
||||
$input_reads \\
|
||||
$cigar_paf \\
|
||||
$set_cigar_bam \\
|
||||
$bam_output
|
||||
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
minimap2: \$(minimap2 --version 2>&1)
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
65
modules/nf-core/modules/minimap2/align/meta.yml
generated
Normal file
65
modules/nf-core/modules/minimap2/align/meta.yml
generated
Normal file
|
@ -0,0 +1,65 @@
|
|||
name: minimap2_align
|
||||
description: A versatile pairwise aligner for genomic and spliced nucleotide sequences
|
||||
keywords:
|
||||
- align
|
||||
- fasta
|
||||
- fastq
|
||||
- genome
|
||||
- paf
|
||||
- reference
|
||||
tools:
|
||||
- minimap2:
|
||||
description: |
|
||||
A versatile pairwise aligner for genomic and spliced nucleotide sequences.
|
||||
homepage: https://github.com/lh3/minimap2
|
||||
documentation: https://github.com/lh3/minimap2#uguide
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- reads:
|
||||
type: file
|
||||
description: |
|
||||
List of input FASTA or FASTQ files of size 1 and 2 for single-end
|
||||
and paired-end data, respectively.
|
||||
- reference:
|
||||
type: file
|
||||
description: |
|
||||
Reference database in FASTA format.
|
||||
- bam_format:
|
||||
type: boolean
|
||||
description: Specify that output should be in BAM format
|
||||
- cigar_paf_format:
|
||||
type: boolean
|
||||
description: Specify that output CIGAR should be in PAF format
|
||||
- cigar_bam:
|
||||
type: boolean
|
||||
description: |
|
||||
Write CIGAR with >65535 ops at the CG tag. This is recommended when
|
||||
doing XYZ (https://github.com/lh3/minimap2#working-with-65535-cigar-operations)
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- paf:
|
||||
type: file
|
||||
description: Alignment in PAF format
|
||||
pattern: "*.paf"
|
||||
- bam:
|
||||
type: file
|
||||
description: Alignment in BAM format
|
||||
pattern: "*.bam"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@heuermh"
|
||||
- "@sofstam"
|
||||
- "@sateeshperi"
|
||||
- "@jfy133"
|
33
modules/nf-core/modules/minimap2/index/main.nf
generated
Normal file
33
modules/nf-core/modules/minimap2/index/main.nf
generated
Normal file
|
@ -0,0 +1,33 @@
|
|||
process MINIMAP2_INDEX {
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? 'bioconda::minimap2=2.21' : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/minimap2:2.21--h5bf99c6_0' :
|
||||
'quay.io/biocontainers/minimap2:2.21--h5bf99c6_0' }"
|
||||
|
||||
input:
|
||||
path fasta
|
||||
|
||||
output:
|
||||
path "*.mmi" , emit: index
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
"""
|
||||
minimap2 \\
|
||||
-t $task.cpus \\
|
||||
-d ${fasta.baseName}.mmi \\
|
||||
$args \\
|
||||
$fasta
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
minimap2: \$(minimap2 --version 2>&1)
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
30
modules/nf-core/modules/minimap2/index/meta.yml
generated
Normal file
30
modules/nf-core/modules/minimap2/index/meta.yml
generated
Normal file
|
@ -0,0 +1,30 @@
|
|||
name: minimap2_index
|
||||
description: Provides fasta index required by minimap2 alignment.
|
||||
keywords:
|
||||
- index
|
||||
- fasta
|
||||
- reference
|
||||
tools:
|
||||
- minimap2:
|
||||
description: |
|
||||
A versatile pairwise aligner for genomic and spliced nucleotide sequences.
|
||||
homepage: https://github.com/lh3/minimap2
|
||||
documentation: https://github.com/lh3/minimap2#uguide
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- fasta:
|
||||
type: file
|
||||
description: |
|
||||
Reference database in FASTA format.
|
||||
output:
|
||||
- mmi:
|
||||
type: file
|
||||
description: Minimap2 fasta index.
|
||||
pattern: "*.mmi"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@yuukiiwa"
|
||||
- "@drpatelh"
|
56
modules/nf-core/modules/samtools/bam2fq/main.nf
generated
Normal file
56
modules/nf-core/modules/samtools/bam2fq/main.nf
generated
Normal file
|
@ -0,0 +1,56 @@
|
|||
process SAMTOOLS_BAM2FQ {
|
||||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
|
||||
'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(inputbam)
|
||||
val split
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.fq.gz"), emit: reads
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
|
||||
if (split){
|
||||
"""
|
||||
samtools \\
|
||||
bam2fq \\
|
||||
$args \\
|
||||
-@ $task.cpus \\
|
||||
-1 ${prefix}_1.fq.gz \\
|
||||
-2 ${prefix}_2.fq.gz \\
|
||||
-0 ${prefix}_other.fq.gz \\
|
||||
-s ${prefix}_singleton.fq.gz \\
|
||||
$inputbam
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
} else {
|
||||
"""
|
||||
samtools \\
|
||||
bam2fq \\
|
||||
$args \\
|
||||
-@ $task.cpus \\
|
||||
$inputbam | gzip --no-name > ${prefix}_interleaved.fq.gz
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
}
|
55
modules/nf-core/modules/samtools/bam2fq/meta.yml
generated
Normal file
55
modules/nf-core/modules/samtools/bam2fq/meta.yml
generated
Normal file
|
@ -0,0 +1,55 @@
|
|||
name: samtools_bam2fq
|
||||
description: |
|
||||
The module uses bam2fq method from samtools to
|
||||
convert a SAM, BAM or CRAM file to FASTQ format
|
||||
keywords:
|
||||
- bam2fq
|
||||
- samtools
|
||||
- fastq
|
||||
tools:
|
||||
- samtools:
|
||||
description: Tools for dealing with SAM, BAM and CRAM files
|
||||
homepage: None
|
||||
documentation: http://www.htslib.org/doc/1.1/samtools.html
|
||||
tool_dev_url: None
|
||||
doi: ""
|
||||
licence: ["MIT"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- inputbam:
|
||||
type: file
|
||||
description: BAM/CRAM/SAM file
|
||||
pattern: "*.{bam,cram,sam}"
|
||||
- split:
|
||||
type: boolean
|
||||
description: |
|
||||
TRUE/FALSE value to indicate if reads should be separated into
|
||||
/1, /2 and if present other, or singleton.
|
||||
Note: choosing TRUE will generate 4 different files.
|
||||
Choosing FALSE will produce a single file, which will be interleaved in case
|
||||
the input contains paired reads.
|
||||
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- reads:
|
||||
type: file
|
||||
description: |
|
||||
FASTQ files, which will be either a group of 4 files (read_1, read_2, other and singleton)
|
||||
or a single interleaved .fq.gz file if the user chooses not to split the reads.
|
||||
pattern: "*.fq.gz"
|
||||
|
||||
authors:
|
||||
- "@lescai"
|
56
modules/nf-core/modules/samtools/view/main.nf
generated
Normal file
56
modules/nf-core/modules/samtools/view/main.nf
generated
Normal file
|
@ -0,0 +1,56 @@
|
|||
process SAMTOOLS_VIEW {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
|
||||
'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(input), path(index)
|
||||
path fasta
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.bam") , emit: bam , optional: true
|
||||
tuple val(meta), path("*.cram"), emit: cram, optional: true
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def args2 = task.ext.args2 ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
def reference = fasta ? "--reference ${fasta} -C" : ""
|
||||
def file_type = input.getExtension()
|
||||
if ("$input" == "${prefix}.${file_type}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
|
||||
"""
|
||||
samtools \\
|
||||
view \\
|
||||
--threads ${task.cpus-1} \\
|
||||
${reference} \\
|
||||
$args \\
|
||||
$input \\
|
||||
$args2 \\
|
||||
> ${prefix}.${file_type}
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
|
||||
stub:
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
"""
|
||||
touch ${prefix}.bam
|
||||
touch ${prefix}.cram
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
57
modules/nf-core/modules/samtools/view/meta.yml
generated
Normal file
57
modules/nf-core/modules/samtools/view/meta.yml
generated
Normal file
|
@ -0,0 +1,57 @@
|
|||
name: samtools_view
|
||||
description: filter/convert SAM/BAM/CRAM file
|
||||
keywords:
|
||||
- view
|
||||
- bam
|
||||
- sam
|
||||
- cram
|
||||
tools:
|
||||
- samtools:
|
||||
description: |
|
||||
SAMtools is a set of utilities for interacting with and post-processing
|
||||
short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
|
||||
These files are generated as output by short read aligners like BWA.
|
||||
homepage: http://www.htslib.org/
|
||||
documentation: hhttp://www.htslib.org/doc/samtools.html
|
||||
doi: 10.1093/bioinformatics/btp352
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- input:
|
||||
type: file
|
||||
description: BAM/CRAM/SAM file
|
||||
pattern: "*.{bam,cram,sam}"
|
||||
- index:
|
||||
type: optional file
|
||||
description: BAM.BAI/CRAM.CRAI file
|
||||
pattern: "*.{.bai,.crai}"
|
||||
- fasta:
|
||||
type: optional file
|
||||
description: Reference file the CRAM was created with
|
||||
pattern: "*.{fasta,fa}"
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bam:
|
||||
type: file
|
||||
description: filtered/converted BAM/SAM file
|
||||
pattern: "*.{bam,sam}"
|
||||
- cram:
|
||||
type: file
|
||||
description: filtered/converted CRAM file
|
||||
pattern: "*.cram"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@drpatelh"
|
||||
- "@joseespinosa"
|
||||
- "@FriederikeHanssen"
|
|
@ -81,6 +81,7 @@ params {
|
|||
shortread_complexityfilter_bbduk_mask = false
|
||||
shortread_complexityfilter_prinseqplusplus_mode = 'entropy'
|
||||
shortread_complexityfilter_prinseqplusplus_dustscore = 0.5
|
||||
shortread_complexityfilter_fastp_threshold = 30
|
||||
save_complexityfiltered_reads = false
|
||||
|
||||
// run merging
|
||||
|
@ -88,12 +89,15 @@ params {
|
|||
save_runmerged_reads = false
|
||||
|
||||
// Host Removal
|
||||
perform_shortread_hostremoval = false
|
||||
shortread_hostremoval_reference = null
|
||||
shortread_hostremoval_index = null
|
||||
save_hostremoval_index = false
|
||||
save_hostremoval_mapped = false
|
||||
save_hostremoval_unmapped = false
|
||||
perform_shortread_hostremoval = false
|
||||
perform_longread_hostremoval = false
|
||||
hostremoval_reference = null
|
||||
shortread_hostremoval_index = null
|
||||
longread_hostremoval_index = null
|
||||
save_hostremoval_index = false
|
||||
save_hostremoval_mapped = false
|
||||
save_hostremoval_unmapped = false
|
||||
|
||||
|
||||
// MALT
|
||||
run_malt = false
|
||||
|
@ -133,11 +137,11 @@ try {
|
|||
|
||||
// Load nf-core/taxprofiler custom profiles from different institutions.
|
||||
// Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs!
|
||||
// try {
|
||||
// includeConfig "${params.custom_config_base}/pipeline/taxprofiler.config"
|
||||
// } catch (Exception e) {
|
||||
// System.err.println("WARNING: Could not load nf-core/config/taxprofiler profiles: ${params.custom_config_base}/pipeline/taxprofiler.config")
|
||||
// }
|
||||
try {
|
||||
includeConfig "${params.custom_config_base}/pipeline/taxprofiler.config"
|
||||
} catch (Exception e) {
|
||||
System.err.println("WARNING: Could not load nf-core/config/taxprofiler profiles: ${params.custom_config_base}/pipeline/taxprofiler.config")
|
||||
}
|
||||
|
||||
|
||||
profiles {
|
||||
|
@ -189,6 +193,8 @@ profiles {
|
|||
}
|
||||
test { includeConfig 'conf/test.config' }
|
||||
test_full { includeConfig 'conf/test_full.config' }
|
||||
test_noprofiling { includeConfig 'conf/test_noprofiling.config' }
|
||||
test_nopreprocessing { includeConfig 'conf/test_preprocessing.config' }
|
||||
}
|
||||
|
||||
// Load igenomes.config if required
|
||||
|
@ -228,7 +234,7 @@ trace {
|
|||
}
|
||||
dag {
|
||||
enabled = true
|
||||
file = "${params.tracedir}/pipeline_dag_${trace_timestamp}.svg"
|
||||
file = "${params.tracedir}/pipeline_dag_${trace_timestamp}.html"
|
||||
}
|
||||
|
||||
manifest {
|
||||
|
|
|
@ -319,7 +319,8 @@
|
|||
},
|
||||
"shortread_complexityfilter_tool": {
|
||||
"type": "string",
|
||||
"default": "bbduk"
|
||||
"default": "bbduk",
|
||||
"enum": ["bbduk", "prinseqplusplus", "fastp"]
|
||||
},
|
||||
"shortread_complexityfilter_bbduk_windowsize": {
|
||||
"type": "integer",
|
||||
|
@ -362,7 +363,10 @@
|
|||
"perform_shortread_hostremoval": {
|
||||
"type": "boolean"
|
||||
},
|
||||
"shortread_hostremoval_reference": {
|
||||
"perform_longread_hostremoval": {
|
||||
"type": "boolean"
|
||||
},
|
||||
"hostremoval_reference": {
|
||||
"type": "string",
|
||||
"default": "None"
|
||||
},
|
||||
|
@ -398,6 +402,14 @@
|
|||
"default": "tsv",
|
||||
"enum": ["blast", "xml", "txt", "daa", "sam", "tsv", "paf"]
|
||||
},
|
||||
"longread_hostremoval_index": {
|
||||
"type": "string",
|
||||
"default": "None"
|
||||
},
|
||||
"shortread_complexityfilter_fastp_threshold": {
|
||||
"type": "integer",
|
||||
"default": 30
|
||||
},
|
||||
"longread_qc_run_clip": {
|
||||
"type": "boolean"
|
||||
},
|
||||
|
@ -415,6 +427,5 @@
|
|||
"longread_qc_targetnbases": {
|
||||
"type": "integer",
|
||||
"default": 500000000
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
47
subworkflows/local/longread_hostremoval.nf
Normal file
47
subworkflows/local/longread_hostremoval.nf
Normal file
|
@ -0,0 +1,47 @@
|
|||
//
|
||||
// Remove host reads via alignment and export off-target reads
|
||||
//
|
||||
|
||||
include { MINIMAP2_INDEX } from '../../modules/nf-core/modules/minimap2/index/main'
|
||||
include { MINIMAP2_ALIGN } from '../../modules/nf-core/modules/minimap2/align/main'
|
||||
include { SAMTOOLS_VIEW } from '../../modules/nf-core/modules/samtools/view/main'
|
||||
include { SAMTOOLS_BAM2FQ } from '../../modules/nf-core/modules/samtools/bam2fq/main'
|
||||
|
||||
workflow LONGREAD_HOSTREMOVAL {
|
||||
take:
|
||||
reads // [ [ meta ], [ reads ] ]
|
||||
reference // /path/to/fasta
|
||||
index // /path/to/index
|
||||
|
||||
main:
|
||||
ch_versions = Channel.empty()
|
||||
ch_multiqc_files = Channel.empty()
|
||||
|
||||
if ( !params.longread_hostremoval_index ) {
|
||||
ch_minimap2_index = MINIMAP2_INDEX ( reference ).index
|
||||
ch_versions = ch_versions.mix( MINIMAP2_INDEX.out.versions )
|
||||
} else {
|
||||
ch_minimap2_index = index
|
||||
}
|
||||
|
||||
MINIMAP2_ALIGN ( reads, ch_minimap2_index, true, false, false )
|
||||
ch_versions = ch_versions.mix( MINIMAP2_ALIGN.out.versions.first() )
|
||||
ch_minimap2_mapped = MINIMAP2_ALIGN.out.bam
|
||||
.map {
|
||||
meta, reads ->
|
||||
[ meta, reads, [] ]
|
||||
}
|
||||
|
||||
|
||||
SAMTOOLS_VIEW ( ch_minimap2_mapped , [] )
|
||||
ch_versions = ch_versions.mix( SAMTOOLS_VIEW.out.versions.first() )
|
||||
|
||||
SAMTOOLS_BAM2FQ ( SAMTOOLS_VIEW.out.bam, false )
|
||||
ch_versions = ch_versions.mix( SAMTOOLS_BAM2FQ.out.versions.first() )
|
||||
|
||||
|
||||
emit:
|
||||
reads = SAMTOOLS_BAM2FQ.out.reads // channel: [ val(meta), [ reads ] ]
|
||||
versions = ch_versions // channel: [ versions.yml ]
|
||||
}
|
||||
|
|
@ -48,7 +48,7 @@ workflow PROFILING {
|
|||
}
|
||||
|
||||
/*
|
||||
PREPARE PROFILER INPUT CHANNELS
|
||||
PREPARE PROFILER INPUT CHANNELS & RUN PROFILING
|
||||
*/
|
||||
|
||||
// Each tool as a slightly different input structure and generally separate
|
||||
|
@ -56,74 +56,27 @@ workflow PROFILING {
|
|||
// for each tool and make liberal use of multiMap to keep reads/databases
|
||||
// channel element order in sync with each other
|
||||
|
||||
// MALT: We groupTuple to have all samples in one channel for MALT as database
|
||||
// loading takes a long time, so we only want to run it once per database
|
||||
// TODO document somewhere we only accept illumina short reads for MALT?
|
||||
ch_input_for_malt = ch_input_for_profiling.malt
|
||||
.filter { it[0]['instrument_platform'] == 'ILLUMINA' }
|
||||
.map {
|
||||
it ->
|
||||
def temp_meta = [ id: it[2]['db_name']] + it[2]
|
||||
def db = it[3]
|
||||
[ temp_meta, it[1], db ]
|
||||
}
|
||||
.groupTuple(by: [0,2])
|
||||
.multiMap {
|
||||
it ->
|
||||
reads: [ it[0], it[1].flatten() ]
|
||||
db: it[2]
|
||||
}
|
||||
|
||||
// All subsequent tools can easily run on a per-sample basis
|
||||
|
||||
ch_input_for_kraken2 = ch_input_for_profiling.kraken2
|
||||
.multiMap {
|
||||
it ->
|
||||
reads: [ it[0] + it[2], it[1] ]
|
||||
db: it[3]
|
||||
}
|
||||
|
||||
ch_input_for_centrifuge = ch_input_for_profiling.centrifuge
|
||||
.filter{
|
||||
if (it[0].is_fasta) log.warn "[nf-core/taxprofiler] Centrifuge currently does not accept FASTA files as input. Skipping Centrifuge for sample ${it[0].id}."
|
||||
!it[0].is_fasta
|
||||
}
|
||||
.multiMap {
|
||||
it ->
|
||||
reads: [ it[0] + it[2], it[1] ]
|
||||
db: it[3]
|
||||
}
|
||||
|
||||
ch_input_for_metaphlan3 = ch_input_for_profiling.metaphlan3
|
||||
.filter{
|
||||
if (it[0].is_fasta) log.warn "[nf-core/taxprofiler] MetaPhlAn3 currently does not accept FASTA files as input. Skipping MetaPhlAn3 for sample ${it[0].id}."
|
||||
!it[0].is_fasta
|
||||
}
|
||||
.multiMap {
|
||||
it ->
|
||||
reads: [it[0] + it[2], it[1]]
|
||||
db: it[3]
|
||||
}
|
||||
|
||||
ch_input_for_kaiju = ch_input_for_profiling.kaiju
|
||||
.multiMap {
|
||||
it ->
|
||||
reads: [it[0] + it[2], it[1]]
|
||||
db: it[3]
|
||||
}
|
||||
|
||||
ch_input_for_diamond = ch_input_for_profiling.diamond
|
||||
.multiMap {
|
||||
it ->
|
||||
reads: [it[0] + it[2], it[1]]
|
||||
db: it[3]
|
||||
}
|
||||
|
||||
/*
|
||||
RUN PROFILING
|
||||
*/
|
||||
|
||||
if ( params.run_malt ) {
|
||||
|
||||
|
||||
// MALT: We groupTuple to have all samples in one channel for MALT as database
|
||||
// loading takes a long time, so we only want to run it once per database
|
||||
// TODO document somewhere we only accept illumina short reads for MALT?
|
||||
ch_input_for_malt = ch_input_for_profiling.malt
|
||||
.filter { it[0]['instrument_platform'] == 'ILLUMINA' }
|
||||
.map {
|
||||
it ->
|
||||
def temp_meta = [ id: it[2]['db_name']] + it[2]
|
||||
def db = it[3]
|
||||
[ temp_meta, it[1], db ]
|
||||
}
|
||||
.groupTuple(by: [0,2])
|
||||
.multiMap {
|
||||
it ->
|
||||
reads: [ it[0], it[1].flatten() ]
|
||||
db: it[2]
|
||||
}
|
||||
|
||||
MALT_RUN ( ch_input_for_malt.reads, params.malt_mode, ch_input_for_malt.db )
|
||||
|
||||
ch_maltrun_for_megan = MALT_RUN.out.rma6
|
||||
|
@ -143,40 +96,94 @@ workflow PROFILING {
|
|||
ch_multiqc_files = ch_multiqc_files.mix( MALT_RUN.out.log.collect{it[1]}.ifEmpty([]) )
|
||||
ch_versions = ch_versions.mix( MALT_RUN.out.versions.first(), MEGAN_RMA2INFO.out.versions.first() )
|
||||
ch_raw_profiles = ch_raw_profiles.mix( MEGAN_RMA2INFO.out.txt )
|
||||
|
||||
}
|
||||
|
||||
if ( params.run_kraken2 ) {
|
||||
|
||||
ch_input_for_kraken2 = ch_input_for_profiling.kraken2
|
||||
.multiMap {
|
||||
it ->
|
||||
reads: [ it[0] + it[2], it[1] ]
|
||||
db: it[3]
|
||||
}
|
||||
|
||||
KRAKEN2_KRAKEN2 ( ch_input_for_kraken2.reads, ch_input_for_kraken2.db )
|
||||
ch_multiqc_files = ch_multiqc_files.mix( KRAKEN2_KRAKEN2.out.txt.collect{it[1]}.ifEmpty([]) )
|
||||
ch_versions = ch_versions.mix( KRAKEN2_KRAKEN2.out.versions.first() )
|
||||
ch_raw_profiles = ch_raw_profiles.mix( KRAKEN2_KRAKEN2.out.txt )
|
||||
|
||||
}
|
||||
|
||||
if ( params.run_centrifuge ) {
|
||||
|
||||
ch_input_for_centrifuge = ch_input_for_profiling.centrifuge
|
||||
.filter{
|
||||
if (it[0].is_fasta) log.warn "[nf-core/taxprofiler] Centrifuge currently does not accept FASTA files as input. Skipping Centrifuge for sample ${it[0].id}."
|
||||
!it[0].is_fasta
|
||||
}
|
||||
.multiMap {
|
||||
it ->
|
||||
reads: [ it[0] + it[2], it[1] ]
|
||||
db: it[3]
|
||||
}
|
||||
|
||||
CENTRIFUGE_CENTRIFUGE ( ch_input_for_centrifuge.reads, ch_input_for_centrifuge.db, params.centrifuge_save_unaligned, params.centrifuge_save_aligned, params.centrifuge_sam_format )
|
||||
CENTRIFUGE_KREPORT (CENTRIFUGE_CENTRIFUGE.out.results, ch_input_for_centrifuge.db)
|
||||
ch_versions = ch_versions.mix( CENTRIFUGE_CENTRIFUGE.out.versions.first() )
|
||||
ch_raw_profiles = ch_raw_profiles.mix( CENTRIFUGE_KREPORT.out.kreport )
|
||||
|
||||
}
|
||||
|
||||
if ( params.run_metaphlan3 ) {
|
||||
|
||||
ch_input_for_metaphlan3 = ch_input_for_profiling.metaphlan3
|
||||
.filter{
|
||||
if (it[0].is_fasta) log.warn "[nf-core/taxprofiler] MetaPhlAn3 currently does not accept FASTA files as input. Skipping MetaPhlAn3 for sample ${it[0].id}."
|
||||
!it[0].is_fasta
|
||||
}
|
||||
.multiMap {
|
||||
it ->
|
||||
reads: [it[0] + it[2], it[1]]
|
||||
db: it[3]
|
||||
}
|
||||
|
||||
METAPHLAN3 ( ch_input_for_metaphlan3.reads, ch_input_for_metaphlan3.db )
|
||||
ch_versions = ch_versions.mix( METAPHLAN3.out.versions.first() )
|
||||
ch_raw_profiles = ch_raw_profiles.mix( METAPHLAN3.out.biom )
|
||||
|
||||
}
|
||||
|
||||
if ( params.run_kaiju ) {
|
||||
|
||||
ch_input_for_kaiju = ch_input_for_profiling.kaiju
|
||||
.multiMap {
|
||||
it ->
|
||||
reads: [it[0] + it[2], it[1]]
|
||||
db: it[3]
|
||||
}
|
||||
|
||||
KAIJU_KAIJU ( ch_input_for_kaiju.reads, ch_input_for_kaiju.db)
|
||||
KAIJU_KAIJU2TABLE (KAIJU_KAIJU.out.results, ch_input_for_kaiju.db, params.kaiju_taxon_name)
|
||||
ch_multiqc_files = ch_multiqc_files.mix( KAIJU_KAIJU2TABLE.out.summary.collect{it[1]}.ifEmpty([]) )
|
||||
ch_versions = ch_versions.mix( KAIJU_KAIJU.out.versions.first() )
|
||||
ch_raw_profiles = ch_raw_profiles.mix( KAIJU_KAIJU2TABLE.out.summary )
|
||||
|
||||
}
|
||||
|
||||
if ( params.run_diamond ) {
|
||||
|
||||
ch_input_for_diamond = ch_input_for_profiling.diamond
|
||||
.multiMap {
|
||||
it ->
|
||||
reads: [it[0] + it[2], it[1]]
|
||||
db: it[3]
|
||||
}
|
||||
|
||||
DIAMOND_BLASTX ( ch_input_for_diamond.reads, ch_input_for_diamond.db, params.diamond_output_format )
|
||||
ch_versions = ch_versions.mix( DIAMOND_BLASTX.out.versions.first() )
|
||||
ch_raw_profiles = ch_raw_profiles.mix( DIAMOND_BLASTX.out.output )
|
||||
|
||||
}
|
||||
|
||||
emit:
|
||||
|
|
|
@ -13,6 +13,7 @@ workflow SHORTREAD_COMPLEXITYFILTERING {
|
|||
ch_versions = Channel.empty()
|
||||
ch_multiqc_files = Channel.empty()
|
||||
|
||||
// fastp complexity filtering is activated via modules.conf in shortread_preprocessing
|
||||
if ( params.shortread_complexityfilter_tool == 'bbduk' ) {
|
||||
ch_filtered_reads = BBMAP_BBDUK ( reads, [] ).reads
|
||||
ch_versions = ch_versions.mix( BBMAP_BBDUK.out.versions.first() )
|
||||
|
|
|
@ -11,7 +11,7 @@ WorkflowTaxprofiler.initialise(params, log)
|
|||
|
||||
// TODO nf-core: Add all file path parameters for the pipeline to the list below
|
||||
// Check input path parameters to see if they exist
|
||||
def checkPathParamList = [ params.input, params.databases, params.shortread_hostremoval_reference,
|
||||
def checkPathParamList = [ params.input, params.databases, params.hostremoval_reference,
|
||||
params.shortread_hostremoval_index, params.multiqc_config
|
||||
]
|
||||
for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
|
||||
|
@ -20,16 +20,18 @@ for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true
|
|||
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.shortread_qc_mergepairs && params.run_malt ) log.warn "[nf-core/taxprofiler] MALT does not accept uncollapsed paired-short reads. Pairs will be profiled as separate files."
|
||||
if (params.shortread_qc_excludeunmerged && !params.shortread_qc_mergepairs) exit 1, "ERROR: [nf-core/taxprofiler] cannot include unmerged reads when merging not turned on. Please specify --shortread_qc_mergepairs"
|
||||
|
||||
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.longread_qc_run_clip || params.longread_qc_run_filter) & !params.perform_longread_qc ) exit 1, "ERROR: [nf-core/taxprofiler] --longread_qc_run_clip or --longread_qc_run_filter requested but quality-control not turned on. Please specify --perform_long_qc"
|
||||
|
||||
if (params.perform_shortread_hostremoval && !params.shortread_hostremoval_reference) { exit 1, "ERROR: [nf-core/taxprofiler] --shortread_hostremoval requested but no --shortread_hostremoval_reference FASTA supplied. Check input." }
|
||||
if (!params.shortread_hostremoval_reference && params.shortread_hostremoval_reference_index) { exit 1, "ERROR: [nf-core/taxprofiler] --shortread_hostremoval_index provided but no --shortread_hostremoval_reference FASTA supplied. Check input." }
|
||||
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.shortread_hostremoval_reference ) { ch_reference = file(params.shortread_hostremoval_reference) }
|
||||
if (params.shortread_hostremoval_index ) { ch_reference_index = file(params.shortread_hostremoval_index ) } else { ch_reference_index = [] }
|
||||
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 ) { ch_reference = file(params.hostremoval_reference) }
|
||||
if (params.shortread_hostremoval_index ) { ch_shortread_reference_index = file(params.shortread_hostremoval_index ) } else { ch_shortread_reference_index = [] }
|
||||
if (params.longread_hostremoval_index ) { ch_longread_reference_index = file(params.longread_hostremoval_index ) } else { ch_longread_reference_index = [] }
|
||||
|
||||
/*
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
@ -49,12 +51,13 @@ ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multi
|
|||
//
|
||||
// SUBWORKFLOW: Consisting of a mix of local and nf-core/modules
|
||||
//
|
||||
include { INPUT_CHECK } from '../subworkflows/local/input_check'
|
||||
include { INPUT_CHECK } from '../subworkflows/local/input_check'
|
||||
|
||||
include { DB_CHECK } from '../subworkflows/local/db_check'
|
||||
include { SHORTREAD_PREPROCESSING } from '../subworkflows/local/shortread_preprocessing'
|
||||
include { LONGREAD_PREPROCESSING } from '../subworkflows/local/longread_preprocessing'
|
||||
include { SHORTREAD_HOSTREMOVAL } from '../subworkflows/local/shortread_hostremoval'
|
||||
include { LONGREAD_HOSTREMOVAL } from '../subworkflows/local/longread_hostremoval'
|
||||
include { SHORTREAD_COMPLEXITYFILTERING } from '../subworkflows/local/shortread_complexityfiltering'
|
||||
include { PROFILING } from '../subworkflows/local/profiling'
|
||||
|
||||
|
@ -132,7 +135,8 @@ workflow TAXPROFILER {
|
|||
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_versions = ch_versions.mix( SHORTREAD_COMPLEXITYFILTERING.out.versions )
|
||||
} else {
|
||||
|
@ -144,16 +148,23 @@ workflow TAXPROFILER {
|
|||
*/
|
||||
|
||||
if ( params.perform_shortread_hostremoval ) {
|
||||
ch_shortreads_hostremoved = SHORTREAD_HOSTREMOVAL ( ch_shortreads_filtered, ch_reference, ch_reference_index ).reads
|
||||
ch_shortreads_hostremoved = SHORTREAD_HOSTREMOVAL ( ch_shortreads_filtered, ch_reference, ch_shortread_reference_index ).reads
|
||||
ch_versions = ch_versions.mix(SHORTREAD_HOSTREMOVAL.out.versions)
|
||||
} else {
|
||||
ch_shortreads_hostremoved = ch_shortreads_filtered
|
||||
}
|
||||
|
||||
if ( params.perform_longread_hostremoval ) {
|
||||
ch_longreads_hostremoved = LONGREAD_HOSTREMOVAL ( ch_longreads_preprocessed, ch_reference, ch_longread_reference_index ).reads
|
||||
ch_versions = ch_versions.mix(LONGREAD_HOSTREMOVAL.out.versions)
|
||||
} else {
|
||||
ch_longreads_hostremoved = ch_longreads_preprocessed
|
||||
}
|
||||
|
||||
if ( params.perform_runmerging ) {
|
||||
|
||||
ch_reads_for_cat_branch = ch_shortreads_hostremoved
|
||||
.mix( ch_longreads_preprocessed )
|
||||
.mix( ch_longreads_hostremoved )
|
||||
.map {
|
||||
meta, reads ->
|
||||
def meta_new = meta.clone()
|
||||
|
@ -185,7 +196,7 @@ workflow TAXPROFILER {
|
|||
|
||||
} else {
|
||||
ch_reads_runmerged = ch_shortreads_hostremoved
|
||||
.mix( ch_longreads_preprocessed, INPUT_CHECK.out.fasta )
|
||||
.mix( ch_longreads_hostremoved, INPUT_CHECK.out.fasta )
|
||||
}
|
||||
|
||||
/*
|
||||
|
@ -222,7 +233,7 @@ workflow TAXPROFILER {
|
|||
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([]) )
|
||||
}
|
||||
|
||||
|
|
Loading…
Reference in a new issue