Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
reads{:bash}
:file
BAM/CRAM/SAM file
*.{bam,cram,sam}
fasta{:bash}
:file
Reference genome in FASTA format
*.{fa,fasta}
fai{:bash}
:file
FASTA index file from samtools faidx
*.{fai}
gzi{:bash}
:file
Optional gzip index file for BAM inputs
*.gzi
Output
name:type
description
pattern
cram{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.{cram,bam}{:bash}
:file
Compressed BAM/CRAM file
*.{cram,bam}
gzi{:bash}
*.gzi{:bash}
:file
gzip index file for BAM outputs
.{bam.gzi}
versions{:bash}
versions.yml{:bash}
:file
File containing software versions
versions.yml
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.
