mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-23 03:28:17 +00:00
71 lines
2.3 KiB
YAML
71 lines
2.3 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
|
||
|
|
params:
|
||
|
|
- outdir:
|
||
|
|
type: string
|
||
|
|
description: |
|
||
|
|
The pipeline's output directory. By default, the module will
|
||
|
|
output files into `$params.outdir/<SOFTWARE>`
|
||
|
|
- publish_dir_mode:
|
||
|
|
type: string
|
||
|
|
description: |
|
||
|
|
Value for the Nextflow `publishDir` mode parameter.
|
||
|
|
Available: symlink, rellink, link, copy, copyNoFollow, move.
|
||
|
|
- enable_conda:
|
||
|
|
type: boolean
|
||
|
|
description: |
|
||
|
|
Run the module with Conda using the software specified
|
||
|
|
via the `conda` directive
|
||
|
|
- singularity_pull_docker_container:
|
||
|
|
type: boolean
|
||
|
|
description: |
|
||
|
|
Instead of directly downloading Singularity images for use with Singularity,
|
||
|
|
force the workflow to pull and convert Docker containers instead.
|
||
|
|
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: "*/*"
|
||
|
|
- version:
|
||
|
|
type: file
|
||
|
|
description: File containing software version
|
||
|
|
pattern: "*.{version.txt}"
|
||
|
|
authors:
|
||
|
|
- "@phue"
|