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"