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
Associated index file for BAM
*.bai
meta2
Groovy Map containing reference information e.g. [ id:'hg38' ]
[ id:'hg38' ]
fasta
Reference sequence in FASTA format. Required for motif (e.g. CpG) filtering
*.fasta
fai
Associated index file for FASTA
*.fai
meta3
Groovy Map containing BED file information e.g. [ id:'regions' ]
[ id:'regions' ]
bed
BED file that will restrict threshold estimation and pileup results to positions overlapping intervals in the file
*.bed
bedgz
*.bed.gz
bgzf-compressed bedMethyl output file(s)
log
*.log
File for debug logs to be written to
versions_modkit
${task.process}
:string
The name of the process
modkit
The name of the tool
modkit --version | sed 's/modkit //'
:eval
The expression to obtain the version of the tool
versions
A bioinformatics tool for working with modified bases in Oxford Nanopore sequencing data
