Description

Writes an interval list created by splitting a reference at Ns.A Program for breaking up a reference into intervals of alternating regions of N and ACGT bases

Input

Name (Type)
Description
Pattern

meta (map)

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

]

fasta (file)

Fasta file to derive the intervals from

*.{fasta,fa,fna}

meta2 (map)

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

]

fai (file)

Index of the fasta file

*.fai

meta3 (map)

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

]

dict (file)

Sequence dictionary of the fasta file

*.dict

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

intervals (file)

The scattered intervals

*.interval_list
maintainer
Github user nvnieuwk
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Tools

picard
MIT

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

broadinstitute.github.io/picard https://github.com/broadinstitute/picard