nf-core_modules/modules/qualimap/bamqc/meta.yml

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1.5 KiB
YAML

name: qualimap_bamqc
description: Evaluate alignment data
keywords:
- quality control
- qc
- bam
tools:
- qualimap:
description: |
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.
homepage: http://qualimap.bioinfo.cipf.es/
documentation: http://qualimap.conesalab.org/doc_html/index.html
doi: 10.1093/bioinformatics/bts503
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: BAM file
pattern: "*.{bam}"
- gff:
type: file
description: Feature file with regions of interest
pattern: "*.{gff,gtf,bed}"
- use_gff:
type: boolean
description: Specifies if feature file should be used or not
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- results:
type: dir
description: Qualimap results dir
pattern: "*/*"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@phue"