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80 lines
2.3 KiB
YAML
80 lines
2.3 KiB
YAML
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name: fastp
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description: Perform adapter/quality trimming on sequencing reads
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keywords:
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- trimming
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- quality control
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- fastq
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tools:
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- fastq:
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description: |
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A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.
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documentation: https://github.com/OpenGene/fastp
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doi: https://doi.org/10.1093/bioinformatics/bty560
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params:
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- outdir:
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type: string
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description: |
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The pipeline's output directory. By default, the module will
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output files into `$params.outdir/<SOFTWARE>`
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- publish_dir_mode:
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type: string
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description: |
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Value for the Nextflow `publishDir` mode parameter.
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Available: symlink, rellink, link, copy, copyNoFollow, move.
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- enable_conda:
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type: boolean
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description: |
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Run the module with Conda using the software specified
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via the `conda` directive
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- singularity_pull_docker_container:
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type: boolean
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description: |
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Instead of directly downloading Singularity images for use with Singularity,
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force the workflow to pull and convert Docker containers instead.
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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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- reads:
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type: file
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description: The trimmed/modified fastq reads
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pattern: "*trim.fastq.gz"
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- json:
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type: file
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description: Results in JSON format
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pattern: "*.json"
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- html:
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type: file
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description: Results in HTML format
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pattern: "*.thml"
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- log:
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type: file
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description: fastq log file
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pattern: "*.log"
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- version:
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type: file
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description: File containing software version
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pattern: "*.{version.txt}"
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- reads_fail:
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type: file
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description: Reads the failed the preprocessing
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pattern: "*fail.fastq.gz"
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authors:
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- "@drpatelh"
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- "@kevinmenden"
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