Description

converts sam/bam/cram/pairs into genome contact map

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

input (file)

BAM/CRAM/SAM file or pairs formatted reads file

*.{bam,cram,sam,pairs.gz}

input (map)

Groovy Map containing sample information
e.g. [ id:‘test2’, single_end

]

input (file)

FASTA file

*.{fasta,fa,fna}

input (file)

Fasta index

*.fai

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

versions (file)

File containing software versions

versions.yml

pretext (file)

pretext map

*.pretext

Tools

pretextmap
MIT

Paired REad TEXTure Mapper. Converts SAM formatted read pairs into genome contact maps.