Trimmomatic (#1757)
* Trimmomatic main only first draft * Add test files * SE PE Adjustment * Remove extra reads input * chore: Remove TODOs * Apply suggestions from code review Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * fix(trimmomatic): Handle SE output correctly Since there's never going to be unpaired reads for SE reads we can get away with it for SE * fix(trimmomatic): Use correct elvis operator to handle logic * fix(trimmomatic): Add hack to work with SE and PE reads * Update test.yml * use the PE and SE trimming correctly * Made user set adaptors * Add documentation * test(trimmomatic): Add files to pytest_modules * test(trimmomatic): Update name of failing test Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com> Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>master
alyssa-ab
2 years ago
committed by
GitHub
parent
8296a28346
commit
c1eb9cce44
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process TRIMMOMATIC {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::trimmomatic=0.39" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/trimmomatic:0.39--hdfd78af_2':
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'quay.io/biocontainers/trimmomatic:0.39--hdfd78af_2' }"
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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("*.paired.trim*.fastq.gz") , emit: trimmed_reads
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tuple val(meta), path("*.unpaired.trim_*.fastq.gz"), optional:true, emit: unpaired_reads
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tuple val(meta), path("*.log") , emit: log
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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 ?: "${meta.id}"
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def trimmed = meta.single_end ? "SE" : "PE"
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def output = meta.single_end ?
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"${prefix}.SE.paired.trim.fastq.gz" // HACK to avoid unpaired and paired in the trimmed_reads output
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: "${prefix}.paired.trim_1.fastq.gz ${prefix}.unpaired.trim_1.fastq.gz ${prefix}.paired.trim_2.fastq.gz ${prefix}.unpaired.trim_2.fastq.gz"
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// TODO Give better error output
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def qual_trim = task.ext.args2 ?: ''
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"""
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trimmomatic \\
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$trimmed \\
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-threads $task.cpus \\
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-trimlog ${prefix}.log \\
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$reads \\
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$output \\
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$qual_trim \\
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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trimmomatic: \$(trimmomatic -version)
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END_VERSIONS
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"""
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}
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name: "trimmomatic"
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description: Performs quality and adapter trimming on paired end and single end reads
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keywords:
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- trimming
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- adapter trimming
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- quality trimming
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tools:
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- "trimmomatic":
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description: "A flexible read trimming tool for Illumina NGS data"
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homepage: "http://www.usadellab.org/cms/?page=trimmomatic"
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documentation: "https://github.com/usadellab/Trimmomatic"
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tool_dev_url: "None"
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doi: "10.1093/bioinformatics/btu170"
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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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Input FastQ files of size 1 or 2 for single-end and paired-end data, respectively.
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pattern: "*.fastq.gz"
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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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- trimmed_reads:
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type: file
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description: The trimmed/modified paired end fastq reads
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pattern: "*.paired.trim*.fastq.gz"
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- unpaired_reads:
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type: file
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description: The trimmed/modified unpaired end fastq reads
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pattern: "*.unpaired.trim_*.fastq.gz"
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- log:
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type: file
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description: trimmomatic log file
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pattern: "*.log"
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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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- "@alyssa-ab"
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@ -0,0 +1,42 @@
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nextflow.enable.dsl = 2
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include {
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TRIMMOMATIC as TRIMMOMATIC_SE
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TRIMMOMATIC as TRIMMOMATIC_PE
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TRIMMOMATIC
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} from '../../../modules/trimmomatic/main.nf'
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//
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// Test with single-end data
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//
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workflow test_trimmomatic_single_end {
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input = [ [ id:'test', single_end:true ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
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]
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TRIMMOMATIC_SE ( input )
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}
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//
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// Test with paired-end data
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//
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workflow test_trimmomatic_paired_end {
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input = [ [ id:'test', single_end:false ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
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]
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TRIMMOMATIC_PE ( input )
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}
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//
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// Failing test with no adaptor
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//
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workflow test_trimmomatic_no_adaptor {
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input = [ [ id:'test', single_end:false ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
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]
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TRIMMOMATIC ( input )
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}
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@ -0,0 +1,12 @@
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process {
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publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
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withName: TRIMMOMATIC_SE {
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ext.args2 = 'ILLUMINACLIP:TruSeq3-SE:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36'
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}
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withName: TRIMMOMATIC_PE {
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ext.args2 = 'ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36'
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}
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}
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@ -0,0 +1,26 @@
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- name: trimmomatic single-end
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command: nextflow run ./tests/modules/trimmomatic -entry test_trimmomatic_single_end -c ./tests/config/nextflow.config -c ./tests/modules/trimmomatic/nextflow.config
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tags:
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- "trimmomatic"
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files:
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- path: "output/trimmomatic/test.SE.paired.trim.fastq.gz"
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- path: "output/trimmomatic/test.log"
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md5sum: e4c3f619e9b0e26847f8f3e3d9af319b
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- name: trimmomatic paired-end
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command: nextflow run ./tests/modules/trimmomatic -entry test_trimmomatic_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/trimmomatic/nextflow.config
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tags:
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- "trimmomatic"
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files:
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- path: "output/trimmomatic/test.log"
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md5sum: 9629761761a34576b3484bf4174f681f
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- path: "output/trimmomatic/test.paired.trim_1.fastq.gz"
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- path: "output/trimmomatic/test.unpaired.trim_1.fastq.gz"
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- path: "output/trimmomatic/test.paired.trim_2.fastq.gz"
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- path: "output/trimmomatic/test.unpaired.trim_2.fastq.gz"
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- name: trimmomatic no adapter specified
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command: nextflow run ./tests/modules/trimmomatic -entry test_trimmomatic_no_adaptor -c ./tests/config/nextflow.config -c ./tests/modules/trimmomatic/nextflow.config
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tags:
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- "trimmomatic"
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exit_code: 1
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