mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 05:43:08 +00:00
e7845e2472
* msisensor2: Add msisensor2 module * msisensor2/scan module added * msisensor2 tests added Changes: - tests added for msisensor2 from the msisensor2 github repo. No available tests from NF-Core test repo. Relates to #1976 * msisensor2 slight bump in stuff * msisensor2: Replaced spelling of 'tumour' with 'tumor' * msisensor2: fix linting, testing and containers Relates to #1976 Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
59 lines
1.8 KiB
YAML
59 lines
1.8 KiB
YAML
name: "msisensor2_msi"
|
|
description: msisensor2 detection of MSI regions.
|
|
keywords:
|
|
- msi
|
|
tools:
|
|
- "msisensor2":
|
|
description: "MSIsensor2 is a novel algorithm based machine learning, featuring a large upgrade in the microsatellite instability (MSI) detection for tumor only sequencing data, including Cell-Free DNA (cfDNA), Formalin-Fixed Paraffin-Embedded(FFPE) and other sample types. The original MSIsensor is specially designed for tumor/normal paired sequencing data."
|
|
homepage: "https://github.com/niu-lab/msisensor2"
|
|
documentation: "https://github.com/niu-lab/msisensor2/blob/master/README.md"
|
|
tool_dev_url: "https://github.com/niu-lab/msisensor2"
|
|
doi: ""
|
|
licence: "GPL-3.0"
|
|
|
|
input:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
#
|
|
- tumor_bam:
|
|
type: file
|
|
description: BAM/CRAM/SAM file
|
|
pattern: "*.{bam,cram,sam}"
|
|
- normal_bam:
|
|
type: file
|
|
description: BAM/CRAM/SAM file
|
|
pattern: "*.{bam,cram,sam}"
|
|
- intervals:
|
|
type: file
|
|
description: BED
|
|
pattern: "*.bed"
|
|
- models:
|
|
type: file
|
|
description: Folder of MSISensor2 models (available from Github or as a product of msisensor2/scan)
|
|
pattern: "*/*"
|
|
|
|
output:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- msi:
|
|
type: file
|
|
description: MSI classifications as a text file
|
|
- distribution:
|
|
type: file
|
|
description: Read count distributions of MSI regions
|
|
- somatic:
|
|
type: file
|
|
description: Somatic MSI regions detected.
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
|
|
authors:
|
|
- "@adamrtalbot"
|