Perform adapter/quality trimming on sequencing reads
Input
name:type
description
pattern
meta{:bash}
: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:false ]
reads{:bash}
: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{:bash}
:file
File in FASTA format containing possible adapters to remove.
*.{fasta,fna,fas,fa}
discard_trimmed_pass{:bash}
: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{:bash}
:boolean
Specify true to save files that failed to pass trimming thresholds ending in *.fail.fastq.gz
save_merged{:bash}
:boolean
Specify true to save all merged reads to a file ending in *.merged.fastq.gz
Output
name:type
description
pattern
reads{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.fastp.fastq.gz{:bash}
:file
The trimmed/modified/unmerged fastq reads
*fastp.fastq.gz
json{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.json{:bash}
:file
Results in JSON format
*.json
html{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.html{:bash}
:file
Results in HTML format
*.html
log{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.log{:bash}
:file
fastq log file
*.log
reads_fail{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.fail.fastq.gz{:bash}
:file
Reads the failed the preprocessing
*fail.fastq.gz
reads_merged{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.merged.fastq.gz{:bash}
:file
Reads that were successfully merged
*.{merged.fastq.gz}
versions{:bash}
versions.yml{:bash}
: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.
