converts sam/bam/cram/pairs into genome contact map
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
input{:bash}
:file
BAM/CRAM/SAM file or pairs formatted reads file
*.{bam,cram,sam,pairs.gz}
meta2{:bash}
fasta{:bash}
Reference sequence file
*.{fasta,fna,fa}
fai{:bash}
Reference sequence index file
*.{fai}
pretext{:bash}
*.pretext{:bash}
pretext map
*.pretext
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
Paired REad TEXTure Mapper. Converts SAM formatted read pairs into genome contact maps.
