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* 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"
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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
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keywords:
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- instrain
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- metagenomics
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- population genomics
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- profile
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tools:
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- instrain:
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description: Calculation of strain-level metrics
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homepage: https://github.com/MrOlm/instrain
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documentation: https://instrain.readthedocs.io/en/latest/
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tool_dev_url: https://github.com/MrOlm/instrain
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doi: 10.1038/s41587-020-00797-0
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licence: ["MIT"]
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input:
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- meta:
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type: map
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description: Groovy Map containing sample information e.g. [ id:'test']
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- bam:
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type: path
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description: Path to .bam file to be profiled
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pattern: "*.{bam,sam}"
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- genome_fasta:
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type: path
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description: Path to .fasta file to be profiled; MUST be the .fasta file that was mapped to to create the .bam file
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pattern: "*.{fasta,fna,fa}"
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- genes_fasta:
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type: path
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description: Path to .fna file of genes to be profiled (OPTIONAL)
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pattern: "*.{fasta,fna,fa}"
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- stb_file:
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type: path
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description: Path to .stb (scaffold to bin) file to be profiled (OPTIONAL)
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pattern: "*.stb"
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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- profile:
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type: path
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description: InStrain profile folder
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pattern: "*.IS/"
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authors:
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- "@mrolm"
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