A windowed adaptive trimming tool for FASTQ files using quality
Input
name:type
description
pattern
meta{:bash}
:map
Groovy Map containing sample information
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. 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{:bash}
: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
single_trimmed{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false, qual:‘Illumina’ ]
${prefix}.se.trimmed.fastq.gz{:bash}
:file
5’ or 3’ trimmed (based on base quality) single-end fastq file
*.se.trimmed.fastq.gz
paired_trimmed{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false, qual:‘Illumina’ ]
${prefix}.pe{1,2}.trimmed.fastq.gz{:bash}
:file
5’ or 3’ trimmed (based on base quality) paired-end fastq files
*.pe{1,2}.trimmed.fastq.gz
singleton_trimmed{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false, qual:‘Illumina’ ]
${prefix}.singleton.trimmed.fastq.gz{:bash}
:file
5’ or 3’ trimmed (based on base quality) singleton fastq file
*.singleton.trimmed.fastq.gz
log{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false, qual:‘Illumina’ ]
*.log{:bash}
:file
log file
*.log
versions{:bash}
versions.yml{:bash}
:file
File containing software versions
versions.yml
Tools
sickle
MIT License
a tool that determines clipping of reads on 3' end and 5'end based on base quality
