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}

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 the 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 demo demultiplex detaxizer mag nascent pathogensurveillance radseq raredisease riboseq rnadnavar rnafusion rnaseq sarek smrnaseq taxprofiler viralrecon
maintainers
Github user drpatelh
Github user kevinmenden
get in touch
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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