Description

Extract the position of the repeats from a soft-masked Fasta file into a BED file, and compress and index it with tabix.

Input

Name
Description
Pattern

ch_fasta (file)

Structure [ val(meta), path(fasta), val(max_seq_length) ] Meta is the Groovy Map containing sample information Fasta is the input Fasta file and max_seq_length is the length of the longest sequence (used to determine which tabix indexes are possible)

Output

Name
Description
Pattern

repeats (file)

Structure: [ val(meta), path(bed.gz), path(bed.gz.gzi), path(tbi)?, path(csi)? ]

Components

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