mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-23 04:49:55 +00:00
73 lines
2.4 KiB
YAML
Generated
73 lines
2.4 KiB
YAML
Generated
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.
|
|
- adapter_fasta:
|
|
type: file
|
|
description: File in FASTA format containing possible adapters to remove.
|
|
pattern: "*.{fasta,fna,fas,fa}"
|
|
- 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"
|