Perform adapter/quality trimming on sequencing reads
Input
name:type
description
pattern
meta:map
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
]
reads:file
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:file
File in FASTA format containing possible adapters to remove.
*.{fasta,fna,fas,fa}
discard_trimmed_pass:boolean
Specify true to not write any reads that pass trimming thresholds. | This can be used to use fastp for the output report only.
save_trimmed_fail:boolean
Specify true to save files that failed to pass trimming thresholds ending in \*.fail.fastq.gz
save_merged:boolean
Specify true to save all merged reads to a file ending in \*.merged.fastq.gz
Output
name:type
description
pattern
reads
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
*.fastp.fastq.gz:file
The trimmed/modified/unmerged fastq reads
*fastp.fastq.gz
json
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
*.json:file
Results in JSON format
*.json
html
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
*.html:file
Results in HTML format
*.html
log
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
*.log:file
fastq log file
*.log
reads_fail
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
*.fail.fastq.gz:file
Reads the failed the preprocessing
*fail.fastq.gz
reads_merged
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
*.merged.fastq.gz:file
Reads that were successfully merged
*.{merged.fastq.gz}
versions
versions.yml:file
File containing software versions
versions.yml
Tools
fastp
MIT
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.
