Description

Advanced sequence file format conversions

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]

reads (file)

BAM/CRAM/SAM file

*.{bam,cram,sam}

fasta (file)

Reference genome in FASTA format

*.{fa,fasta}

fai (file)

FASTA index file from samtools faidx

*.{fai}

gzi (file)

Optional gzip index file for BAM inputs

*.gzi

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]

versions (file)

File containing software versions

versions.yml

reads (file)

Converted reads

*.{sam, bam, cram}

gzi (Optional file)

gzip index file for BAM outputs

.{bam.gzi}
author
Github user matthdsm
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Tools

scramble
BSD

Staden Package 'io_lib' (sometimes referred to as libstaden-read by distributions). This contains code for reading and writing a variety of Bioinformatics / DNA Sequence formats.

github.com/jkbonfield/io_lib github.com/jkbonfield/io_lib/blob/master/README.md https://github.com/jkbonfield/io_lib