mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-10 21:03:09 +00:00
Add Falco as an alternative to FastQC
This commit is contained in:
parent
4f27998852
commit
8eddb32b88
12 changed files with 217 additions and 22 deletions
1
.github/workflows/ci.yml
vendored
1
.github/workflows/ci.yml
vendored
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@ -23,6 +23,7 @@ jobs:
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- "21.10.3"
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- "latest-everything"
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parameters:
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- "--perform_fastqc_alternative false"
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- "--perform_longread_qc false"
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- "--perform_shortread_qc false"
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- "--shortread_qc_tool fastp"
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@ -62,6 +62,10 @@
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- [FILTLONG](https://github.com/rrwick/Filtlong)
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- [Falco](https://doi.org/10.12688/f1000research.21142.2)
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> de Sena Brandine G and Smith AD. Falco: high-speed FastQC emulation for quality control of sequencing data. F1000Research 2021, 8:1874
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## Software packaging/containerisation tools
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- [Anaconda](https://anaconda.com)
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@ -30,7 +30,7 @@ On release, automated continuous integration tests run the pipeline on a full-si
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![](docs/images/taxprofiler_tube.png)
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1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
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1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) or [`Falco`](https://github.com/smithlabcode/falco) as an alternative option)
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2. Performs optional read pre-processing
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- Adapter clipping and merging (short-read: [fastp](https://github.com/OpenGene/fastp), [AdapterRemoval2](https://github.com/MikkelSchubert/adapterremoval); long-read: [porechop](https://github.com/rrwick/Porechop))
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- Low complexity and quality filtering (short-read: [bbduk](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/), [PRINSEQ++](https://github.com/Adrian-Cantu/PRINSEQ-plus-plus); long-read: [Filtlong](https://github.com/rrwick/Filtlong))
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@ -40,6 +40,24 @@ process {
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]
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}
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withName: FALCO {
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ext.prefix = { "${meta.id}_${meta.run_accession}_raw" }
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publishDir = [
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path: { "${params.outdir}/falco/raw" },
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mode: params.publish_dir_mode,
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pattern: '*.{html,txt}'
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]
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}
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withName: FALCO_PROCESSED {
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ext.prefix = { "${meta.id}_${meta.run_accession}_processed" }
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publishDir = [
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path: { "${params.outdir}/falco/processed" },
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mode: params.publish_dir_mode,
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pattern: '*.{html,txt}'
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]
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}
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withName: FASTP_SINGLE {
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ext.args = [
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// trimming options
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@ -165,7 +165,9 @@ work # Directory containing the nextflow working files
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.nextflow_log # Log file from Nextflow
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# Other nextflow hidden files, eg. history of pipeline runs and old logs.
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```
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### Sequencing quality control
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nf-core taxprofiler offers [`Falco`](https://github.com/smithlabcode/falco] as an alternative option to [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
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### Preprocessing Steps
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nf-core/taxprofiler offers four main preprocessing steps
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@ -179,7 +181,7 @@ nf-core/taxprofiler offers four main preprocessing steps
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Raw sequencing read processing in the form of adapter clipping and paired-end read merging can be activated via the `--perform_shortread_qc` or `--perform_longread_qc` flags.
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It is highly recommended to run this on raw reads to remove artefacts from sequencing that can cause false positive identification of taxa (e.g. contaminated reference genomes) and/or skews in taxonomic abundance profiles.
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It is highly recommended to run this on raw reads to remove artifacts from sequencing that can cause false positive identification of taxa (e.g. contaminated reference genomes) and/or skews in taxonomic abundance profiles.
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There are currently two options for short-read preprocessing: `fastp` or `adapterremoval`.
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@ -49,6 +49,10 @@
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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},
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"falco": {
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"branch": "master",
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"git_sha": "fc959214036403ad83efe7a41d43d0606c445cda"
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},
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"fastp": {
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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57
modules/nf-core/falco/main.nf
generated
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57
modules/nf-core/falco/main.nf
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@ -0,0 +1,57 @@
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process FALCO {
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tag "$meta.id"
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label 'process_single'
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conda (params.enable_conda ? "bioconda::falco=1.2.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/falco:1.2.1--h867801b_3':
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'quay.io/biocontainers/falco:1.2.1--h867801b_3' }"
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input:
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tuple val(meta), path(reads)
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output:
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tuple val(meta), path("*.html"), emit: html
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tuple val(meta), path("*.txt") , emit: txt
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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if ( reads.toList().size() == 1 ) {
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"""
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falco $args --threads $task.cpus ${reads} -D ${prefix}_data.txt -S ${prefix}_summary.txt -R ${prefix}_report.html
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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falco:\$( falco --version | sed -e "s/falco//g" )
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END_VERSIONS
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"""
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} else {
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"""
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falco $args --threads $task.cpus ${reads}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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falco:\$( falco --version | sed -e "s/falco//g" )
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END_VERSIONS
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"""
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}
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stub:
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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touch ${prefix}_data.txt
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touch ${prefix}_fastqc_data.html
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touch ${prefix}_summary.txt
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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falco: \$( falco --version | sed -e "s/falco v//g" )
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END_VERSIONS
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"""
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}
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52
modules/nf-core/falco/meta.yml
generated
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52
modules/nf-core/falco/meta.yml
generated
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name: falco
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description: Run falco on sequenced reads
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keywords:
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- quality control
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- qc
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- adapters
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- fastq
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tools:
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- fastqc:
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description: "falco is a drop-in C++ implementation of FastQC to assess the quality of sequence reads."
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homepage: "https://falco.readthedocs.io/"
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documentation: "https://falco.readthedocs.io/"
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tool_dev_url: "None"
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doi: ""
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licence: "['GPL v3']"
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- reads:
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type: file
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description: |
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List of input FastQ files of size 1 and 2 for single-end and paired-end data,
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respectively.
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- html:
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type: file
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description: FastQC like report
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pattern: "*_{fastqc_report.html}"
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- txt:
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type: file
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description: falco report data
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pattern: "*_{data.txt}"
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- txt:
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type: file
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description: falco summary file
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pattern: "*_{summary.txt}"
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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authors:
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- "@lucacozzuto"
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@ -10,7 +10,11 @@
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"type": "object",
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"fa_icon": "fas fa-terminal",
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"description": "Define where the pipeline should find input data and save output data.",
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"required": ["input", "outdir", "databases"],
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"required": [
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"input",
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"outdir",
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"databases"
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],
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"properties": {
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"input": {
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"type": "string",
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"shortread_qc_tool": {
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"type": "string",
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"default": "fastp",
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"enum": ["fastp", "adapterremoval"],
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"enum": [
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"fastp",
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"adapterremoval"
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],
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"fa_icon": "fas fa-tools",
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"description": "Specify which tool to use for short-read QC"
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},
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@ -133,7 +140,11 @@
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"shortread_complexityfilter_tool": {
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"type": "string",
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"default": "bbduk",
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"enum": ["bbduk", "prinseqplusplus", "fastp"],
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"enum": [
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"bbduk",
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"prinseqplusplus",
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"fastp"
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],
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"fa_icon": "fas fa-hammer",
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"description": "Specify which tool to use for complexity filtering"
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},
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"shortread_complexityfilter_prinseqplusplus_mode": {
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"type": "string",
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"default": "entropy",
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"enum": ["entropy", "dust"],
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"enum": [
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"entropy",
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"dust"
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],
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"fa_icon": "fas fa-check-square",
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"description": "Specify the complexity filter mode for PRINSEQ++"
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},
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@ -341,7 +355,15 @@
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"diamond_output_format": {
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"type": "string",
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"default": "tsv",
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"enum": ["blast", "xml", "txt", "daa", "sam", "tsv", "paf"],
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"enum": [
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"blast",
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"xml",
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"txt",
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"daa",
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"sam",
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"tsv",
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"paf"
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],
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"fa_icon": "fas fa-file",
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"description": "Specify output format from DIAMOND profiling.",
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"help_text": "DIAMOND can produce output in a number of different formats, you can specify here which to produce.\n\nNote that DIAMOND can only produce one format at a time, and depending on which you pick, some downstream steps may not be executed. For example, selecting `daa` or `sam` will mean you will not get a tabular taxonomic profile as with the other tools.\n\nWill be overriden by `--diamond_save_reads.`\n\n> Modifies tool parameter(s):\n> - diamond blastx: `--outfmt`"
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@ -360,7 +382,14 @@
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"kaiju_taxon_rank": {
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"type": "string",
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"default": "species",
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"enum": ["phylum", "class", "order", "family", "genus", "species"],
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"enum": [
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"phylum",
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"class",
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"order",
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"family",
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"genus",
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"species"
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],
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"fa_icon": "fas fa-tag",
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"description": "Specify taxonomic rank to be displayed in Kaiju taxon table",
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"help_text": "Specify the taxonomic level(s) to be displayed in the resulting Kaiju taxon table, as generated by the kaiju2table helper tool.\n\nThis can be either a single level (e.g. `species`), or a comma separated list to display the full taxonomic path (e.g. `superkingdom,phylum,class,order,family,genus,species.`).\n\n> Modifies tool parameter(s):\n> - kaiju2table: `-l`"
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@ -555,7 +584,14 @@
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"description": "Method used to save pipeline results to output directory.",
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"help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
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"fa_icon": "fas fa-copy",
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"enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
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"enum": [
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"symlink",
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"rellink",
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"link",
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"copy",
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"copyNoFollow",
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"move"
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],
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"hidden": true
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},
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"email_on_fail": {
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@ -3,6 +3,8 @@
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//
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include { FASTQC as FASTQC_PROCESSED } from '../../modules/nf-core/fastqc/main'
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include { FALCO as FALCO_PROCESSED } from '../../modules/nf-core/falco/main'
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include { PORECHOP } from '../../modules/nf-core/porechop/main'
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include { FILTLONG } from '../../modules/nf-core/filtlong/main'
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@ -52,8 +54,14 @@ workflow LONGREAD_PREPROCESSING {
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ch_multiqc_files = ch_multiqc_files.mix( FILTLONG.out.log )
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}
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FASTQC_PROCESSED ( ch_processed_reads )
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ch_multiqc_files = ch_multiqc_files.mix( FASTQC_PROCESSED.out.zip )
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if (params.perform_fastqc_alternative) {
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FALCO_PROCESSED ( ch_processed_reads )
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ch_multiqc_files = ch_multiqc_files.mix( FALCO_PROCESSED.out.txt )
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} else {
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FASTQC_PROCESSED ( ch_processed_reads )
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ch_multiqc_files = ch_multiqc_files.mix( FASTQC_PROCESSED.out.zip )
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}
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emit:
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reads = ch_processed_reads // channel: [ val(meta), [ reads ] ]
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@ -5,7 +5,8 @@
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include { SHORTREAD_FASTP } from './shortread_fastp'
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include { SHORTREAD_ADAPTERREMOVAL } from './shortread_adapterremoval'
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include { FASTQC as FASTQC_PROCESSED } from '../../modules/nf-core/fastqc/main'
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include { FASTQC as FASTQC_PROCESSED } from '../../modules/nf-core/fastqc/main'
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include { FALCO as FALCO_PROCESSED } from '../../modules/nf-core/falco/main'
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workflow SHORTREAD_PREPROCESSING {
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take:
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ch_processed_reads = reads
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}
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FASTQC_PROCESSED ( ch_processed_reads )
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ch_versions = ch_versions.mix( FASTQC_PROCESSED.out.versions )
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ch_multiqc_files = ch_multiqc_files.mix( FASTQC_PROCESSED.out.zip )
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if (params.perform_fastqc_alternative) {
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FALCO_PROCESSED ( ch_processed_reads )
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ch_versions = ch_versions.mix( FALCO_PROCESSED.out.versions )
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ch_multiqc_files = ch_multiqc_files.mix( FALCO_PROCESSED.out.txt )
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} else {
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FASTQC_PROCESSED ( ch_processed_reads )
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ch_versions = ch_versions.mix( FASTQC_PROCESSED.out.versions )
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ch_multiqc_files = ch_multiqc_files.mix( FASTQC_PROCESSED.out.zip )
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}
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emit:
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reads = ch_processed_reads // channel: [ val(meta), [ reads ] ]
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@ -84,6 +84,7 @@ include { STANDARDISATION_PROFILES } from '../subworkflows/local/standardis
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// MODULE: Installed directly from nf-core/modules
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//
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include { FASTQC } from '../modules/nf-core/fastqc/main'
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include { FALCO } from '../modules/nf-core/falco/main'
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include { MULTIQC } from '../modules/nf-core/multiqc/main'
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include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main'
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include { CAT_FASTQ } from '../modules/nf-core/cat/fastq/main'
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*/
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ch_input_for_fastqc = INPUT_CHECK.out.fastq.mix( INPUT_CHECK.out.nanopore )
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FASTQC (
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ch_input_for_fastqc
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)
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ch_versions = ch_versions.mix(FASTQC.out.versions.first())
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if ( params.perform_fastqc_alternative ) {
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FALCO ( ch_input_for_fastqc )
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ch_versions = ch_versions.mix(FALCO.out.versions.first())
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} else {
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FASTQC ( ch_input_for_fastqc )
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ch_versions = ch_versions.mix(FASTQC.out.versions.first())
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}
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/*
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SUBWORKFLOW: PERFORM PREPROCESSING
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*/
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@ -254,7 +256,10 @@ workflow TAXPROFILER {
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ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
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ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml'))
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ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
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ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
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if (!params.perform_fastqc_alternative) {
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ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
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}
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if (params.perform_shortread_qc) {
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ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) )
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