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:false]
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
single_trimmed
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false, qual:‘Illumina’ ]
*.se.trimmed.fastq.gz
:file
Single end trimmed reads
*.se.trimmed.fastq.gz
paired_trimmed
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false, qual:‘Illumina’ ]
*.pe{1,2}.trimmed.fastq.gz
:file
Paired end trimmed reads
*.pe{1,2}.trimmed.fastq.gz
singleton_trimmed
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false, qual:‘Illumina’ ]
*.singleton.trimmed.fastq.gz
:file
Singleton trimmed reads
*.singleton.trimmed.fastq.gz
log
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false, qual:‘Illumina’ ]
*.log
:file
log file
*.log
versions_sickle
${task.process}
:string
The process the versions were collected from
sickle
:string
The tool name
sickle --version 2>&1 | head -1 | sed "s/sickle version //"
:eval
The expression to obtain the version of the tool
Topics
name:type
description
pattern
versions
${task.process}
:string
The process the versions were collected from
sickle
:string
The tool name
sickle --version 2>&1 | head -1 | sed "s/sickle version //"
:eval
The expression to obtain the version of the tool
Tools
sickle
MIT License
a tool that determines clipping of reads on 3' end and 5'end based on base quality
