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.
Output
name:type
description
pattern
reads
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*{3prime,5prime,trimmed,val}{,_1,_2}.fq.gz:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*{3prime,5prime,trimmed,val}{,_1,_2}.fq.gz
log
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*_{report.txt}
*report.txt:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*_{report.txt}
unpaired
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*unpaired{,_1,_2}.fq.gz:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*unpaired*.fq.gz
html
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*_{fastqc.html}
*.html:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*_{fastqc.html}
zip
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*_{fastqc.zip}
*.zip:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*_{fastqc.zip}
versions
versions.yml:file
File containing software versions
versions.yml
Tools
trimgalore
GPL-3.0-or-later
A wrapper tool around Cutadapt and FastQC to consistently apply quality
and adapter trimming to FastQ files, with some extra functionality for
MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.
