Allows one to screen for overlaps between two sets of genomic features.
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
intervals1
:file
BAM/BED/GFF/VCF
*.{bed|gff|vcf}
intervals2
meta2
Groovy Map containing reference chromosome sizes e.g. [ id:‘test’ ]
chrom_sizes
Chromosome sizes file
*{.sizes,.txt}
mapped
*.${extension}
File containing the description of overlaps found between the features in A and the features in B, with statistics
versions_bedtools
${task.process}
:string
The name of the process
bedtools
The name of the tool
bedtools --version | sed -e 's/bedtools v//g'
:eval
The expression to obtain the version of the tool
versions
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
