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