nf-core_modules/modules/fastp/meta.yml

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name: fastp
description: Perform adapter/quality trimming on sequencing reads
keywords:
- trimming
- quality control
- fastq
tools:
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- fastp:
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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"]
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input:
- meta:
type: map
description: |
Groovy Map containing sample information
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.
- 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`
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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
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pattern: "*trim.fastq.gz"
- json:
type: file
description: Results in JSON format
pattern: "*.json"
- html:
type: file
description: Results in HTML format
pattern: "*.html"
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- log:
type: file
description: fastq log file
pattern: "*.log"
- versions:
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type: file
description: File containing software versions
pattern: "versions.yml"
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- 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}"
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authors:
- "@drpatelh"
- "@kevinmenden"