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