Extracts per-base methylation metrics from alignments
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
bam{:bash}
:file
BAM/CRAM file
*.{bam,cram}
meta2{:bash}
bai{:bash}
BAM/CRAM index file
*.{bai,crai}
meta3{:bash}
fasta{:bash}
Input genome fasta file
*.{fasta,fa}
meta4{:bash}
fai{:bash}
FASTA index file
*.{fai}
bedgraph{:bash}
*.bedGraph{:bash}
bedGraph file, containing per-base methylation metrics
*.bedGraph
methylkit{:bash}
*.methylKit{:bash}
methylKit file, containing per-base methylation metrics
*.methylKit
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
Methylation caller from MethylDackel, a (mostly) universal methylation extractor for methyl-seq experiments.
