Description

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

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

reads (file)

The trimmed/modified/unmerged fastq reads

*fastp.fastq.gz

json (file)

Results in JSON format

*.json

html (file)

Results in HTML format

*.html

log (file)

fastq log file

*.log

versions (file)

File containing software versions

versions.yml

reads_fail (file)

Reads the failed the preprocessing

*fail.fastq.gz

reads_merged (file)

Reads that were successfully merged

*.{merged.fastq.gz}
included in
airrflow bacass demultiplex denovotranscript detaxizer mag nascent pathogensurveillance radseq raredisease riboseq rnadnavar rnafusion rnaseq sarek smrnaseq taxprofiler viralrecon
maintainers
Github user drpatelh
Github user kevinmenden
get in touch
Ask a question on Slack Open an issue on GitHub

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.

github.com/OpenGene/fastp 10.1093/bioinformatics/bty560