mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
031fbd37aa
* add instrain profile * module instrain/profile * add instrain profile * module instrain/profile * instrain profile * Update modules/instrain/profile/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/instrain/profile/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/instrain/profile/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/instrain/profile/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/instrain/profile/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/instrain/profile/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/instrain/profile/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * update * linting * Apply suggestions from code review * Update modules/instrain/profile/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
54 lines
1.7 KiB
YAML
54 lines
1.7 KiB
YAML
name: "instrain_profile"
|
|
description: inStrain is python program for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification
|
|
keywords:
|
|
- instrain
|
|
- metagenomics
|
|
- population genomics
|
|
- profile
|
|
tools:
|
|
- instrain:
|
|
description: Calculation of strain-level metrics
|
|
homepage: https://github.com/MrOlm/instrain
|
|
documentation: https://instrain.readthedocs.io/en/latest/
|
|
tool_dev_url: https://github.com/MrOlm/instrain
|
|
doi: 10.1038/s41587-020-00797-0
|
|
licence: ["MIT"]
|
|
|
|
input:
|
|
- meta:
|
|
type: map
|
|
description: Groovy Map containing sample information e.g. [ id:'test']
|
|
- bam:
|
|
type: path
|
|
description: Path to .bam file to be profiled
|
|
pattern: "*.{bam,sam}"
|
|
- genome_fasta:
|
|
type: path
|
|
description: Path to .fasta file to be profiled; MUST be the .fasta file that was mapped to to create the .bam file
|
|
pattern: "*.{fasta,fna,fa}"
|
|
- genes_fasta:
|
|
type: path
|
|
description: Path to .fna file of genes to be profiled (OPTIONAL)
|
|
pattern: "*.{fasta,fna,fa}"
|
|
- stb_file:
|
|
type: path
|
|
description: Path to .stb (scaffold to bin) file to be profiled (OPTIONAL)
|
|
pattern: "*.stb"
|
|
|
|
output:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
- profile:
|
|
type: path
|
|
description: InStrain profile folder
|
|
pattern: "*.IS/"
|
|
|
|
authors:
|
|
- "@mrolm"
|