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taxprofiler/modules/nf-core/fastp/meta.yml
2022-10-05 12:21:54 +02:00

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name: fastp
description: Perform adapter/quality trimming on sequencing reads
keywords:
- trimming
- quality control
- fastq
tools:
- fastp:
description: |
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.
documentation: https://github.com/OpenGene/fastp
doi: https://doi.org/10.1093/bioinformatics/bty560
licence: ["MIT"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information. Use 'single_end: true' to specify single ended or interleaved FASTQs. Use 'single_end: false' for paired-end reads.
e.g. [ id:'test', single_end:false ]
- reads:
type: file
description: |
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively. If you wish to run interleaved paired-end data, supply as single-end data
but with `--interleaved_in` in your `modules.conf`'s `ext.args` for the module.
- save_trimmed_fail:
type: boolean
description: Specify true to save files that failed to pass trimming thresholds ending in `*.fail.fastq.gz`
- save_merged:
type: boolean
description: Specify true to save all merged reads to the a file ending in `*.merged.fastq.gz`
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- reads:
type: file
description: The trimmed/modified/unmerged fastq reads
pattern: "*fastp.fastq.gz"
- json:
type: file
description: Results in JSON format
pattern: "*.json"
- html:
type: file
description: Results in HTML format
pattern: "*.html"
- log:
type: file
description: fastq log file
pattern: "*.log"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- reads_fail:
type: file
description: Reads the failed the preprocessing
pattern: "*fail.fastq.gz"
- reads_merged:
type: file
description: Reads that were successfully merged
pattern: "*.{merged.fastq.gz}"
authors:
- "@drpatelh"
- "@kevinmenden"