Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
cram{:bash}
:file
Input cram file
*.{cram}
crai{:bash}
:file
Index file for cram file
*.{crai}
gff{:bash}
:file
Feature file with regions of interest
*.{gff,gtf,bed}
fasta{:bash}
:file
Reference file of cram file
*.{fasta,fa,fna}
fasta_fai{:bash}
:file
Index file for reference file
*.{fai}
Output
name:type
description
pattern
results{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
${prefix}{:bash}
:directory
Qualimap results dir
*/*
versions{:bash}
versions.yml{:bash}
:file
File containing software versions
versions.yml
Tools
qualimap
GPL-2.0-only
Qualimap 2 is a platform-independent application written in
Java and R that provides both a Graphical User Interface and
a command-line interface to facilitate the quality control of
alignment sequencing data and its derivatives like feature counts.
