Description

A windowed adaptive trimming tool for FASTQ files using quality

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
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. File of forward reads must be supplied first and reverse reads as the second e.g. [“read.1.fastq.gz”,“read.2.fastq.gz”]

*.{fq,fastq,fq.gz,fastq.gz}

qual_type (string)

sickle needs a base quality values, which could be either illumina, solexa or sanger

illumina or solexa or sanger

Output

Name (Type)
Description
Pattern

meta (map)

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

, qual:‘Illumina’ ]

single_trimmed (file)

5’ or 3’ trimmed (based on base quality) single-end fastq file

*.se.trimmed.fastq.gz

paired1_trimmed (file)

5’ or 3’ trimmed (based on base quality) R1 fastq file

*.pe1.trimmed.fastq.gz

paired2_trimmed (file)

5’ or 3’ trimmed (based on base quality) R2 fastq file

*.pe2.trimmed.fastq.gz

log (file)

log file

*.log

versions (file)

File containing software versions

versions.yml
author
Github user BioInf2305
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

sickle
MIT License

a tool that determines clipping of reads on 3' end and 5'end based on base quality

github.com/najoshi/sickle https://github.com/najoshi/sickle