Performs alignment of BS-Seq reads using bismark
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.
meta2:map
fasta:file
Reference genome FASTA file
meta3:map
index:directory
Bismark genome index directory
BismarkIndex
bam
*bam:file
Output BAM file containing read alignments
*.{bam}
report
*report.txt:file
Bismark alignment reports
*{report.txt}
unmapped
*fq.gz:file
Output FastQ file(s) containing unmapped reads
*.{fq.gz}
versions
versions.yml:file
File containing software versions
versions.yml
Bismark is a tool to map bisulfite treated sequencing reads and perform methylation calling in a quick and easy-to-use fashion.
