Performs alignment of BS-Seq reads using bismark
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.
meta2{:bash}
fasta{:bash}
Reference genome FASTA file
meta3{:bash}
index{:bash}
:directory
Bismark genome index directory
BismarkIndex
bam{:bash}
*bam{:bash}
Output BAM file containing read alignments
*.{bam}
report{:bash}
*report.txt{:bash}
Bismark alignment reports
*{report.txt}
unmapped{:bash}
*fq.gz{:bash}
Output FastQ file(s) containing unmapped reads
*.{fq.gz}
versions_bismark{:bash}
${task.process}{:bash}
:string
The name of the process
bismark{:bash}
The name of the tool
bismark -v 2>&1 | sed -n 's/^.*Bismark Version: v//p'{:bash}
:eval
The expression to obtain the version of the tool
versions{:bash}
Bismark is a tool to map bisulfite treated sequencing reads and perform methylation calling in a quick and easy-to-use fashion.
