Trim FastQ files using Trim Galore!
meta
Groovy Map containing sample information e.g. [ id:‘test’, single_end
reads
List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.
List of input adapter trimmed FastQ files of size 1 and 2 for single-end and paired-end data, respectively.
*{3prime,5prime,trimmed,val}*.fq.gz
unpaired
FastQ files containing unpaired reads from read 1 or read 2
*unpaired*.fq.gz
html
FastQC report (optional)
*_{fastqc.html}
zip
FastQC report archive (optional)
*_{fastqc.zip}
log
Trim Galore! trimming report
*_{report.txt}
versions
File containing software versions
versions.yml
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.
