A bioinformatics tool for working with modified bases
meta:map
Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
[ id:'test', single_end:false ]
bam:file
Sorted BAM/CRAM file
*.{bam,cram}
bai:file
Associated index file for BAM
*.bai
meta2:map
Groovy Map containing reference information e.g. [ id:'hg38' ]
[ id:'hg38' ]
fasta:file
Reference sequence in FASTA format. Required for motif (e.g. CpG) filtering
*.fasta
meta3:map
Groovy Map containing BED file information e.g. [ id:'regions' ]
[ id:'regions' ]
bed:file
BED file that will restrict threshold estimation and pileup results to positions overlapping intervals in the file
*.bed
bed
*.bed:file
bedMethyl output file(s)
bedgraph
*.bedgraph:file
bedgraph output files
*.bedgraph
log
*.log:file
File for debug logs to be written to
*.log
versions
versions.yml:file
File containing software versions
versions.yml
A bioinformatics tool for working with modified bases in Oxford Nanopore sequencing data
