Find ligation junctions in .sam, make .pairs
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
bam{:bash}
:file
BAM/CRAM/SAM file
*.{bam,cram,sam}
chromsizes{:bash}
chromosome size file
pairsam{:bash}
*.pairsam.gz{:bash}
parsed pair file
*.{pairsam.gz}
stat{:bash}
*.pairsam.stat{:bash}
stats of the pairs
*.{pairsam.stat}
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
CLI tools to process mapped Hi-C data
