name: ngscheckmate_ncm
description: Determining whether sequencing data comes from the same individual by
  using SNP matching. Designed for humans on vcf or bam files.
keywords:
  - ngscheckmate
  - matching
  - snp
tools:
  - ngscheckmate:
      description: NGSCheckMate is a software package for identifying next generation
        sequencing (NGS) data files from the same individual, including matching between
        DNA and RNA.
      homepage: https://github.com/parklab/NGSCheckMate
      documentation: https://github.com/parklab/NGSCheckMate
      tool_dev_url: https://github.com/parklab/NGSCheckMate
      doi: "10.1093/nar/gkx193"
      licence: ["MIT"]
      identifier: biotools:ngscheckmate
input:
  - - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'test']
    - files:
        type: file
        description: VCF or BAM files for each sample, in a merged channel (possibly
          gzipped). BAM files require an index too.
        pattern: "*.{vcf,vcf.gz,bam,bai}"
  - - meta2:
        type: map
        description: |
          Groovy Map containing SNP information
          e.g. [ id:'test' ]
    - snp_bed:
        type: file
        description: BED file containing the SNPs to analyse
        pattern: "*.{bed}"
  - - meta3:
        type: map
        description: |
          Groovy Map containing reference fasta index information
          e.g. [ id:'test' ]
    - fasta:
        type: file
        description: fasta file for the genome, only used in the bam mode
        pattern: "*.{bed}"
output:
  - corr_matrix:
      - meta:
          type: file
          description: A text file containing the correlation matrix between each sample
          pattern: "*corr_matrix.txt"
      - "*_corr_matrix.txt":
          type: file
          description: A text file containing the correlation matrix between each sample
          pattern: "*corr_matrix.txt"
  - matched:
      - meta:
          type: file
          description: A txt file containing only the samples that match with each other
          pattern: "*matched.txt"
      - "*_matched.txt":
          type: file
          description: A txt file containing only the samples that match with each other
          pattern: "*matched.txt"
  - all:
      - meta:
          type: file
          description: A txt file containing all the sample comparisons, whether they
            match or not
          pattern: "*all.txt"
      - "*_all.txt":
          type: file
          description: A txt file containing all the sample comparisons, whether they
            match or not
          pattern: "*all.txt"
  - pdf:
      - meta:
          type: file
          description: A pdf containing a dendrogram showing how the samples match up
          pattern: "*.{pdf}"
      - "*.pdf":
          type: file
          description: A pdf containing a dendrogram showing how the samples match up
          pattern: "*.{pdf}"
  - vcf:
      - meta:
          type: file
          description: If ran in bam mode, vcf files for each sample giving the SNP calls
            used
          pattern: "*.vcf"
      - "*.vcf":
          type: file
          description: If ran in bam mode, vcf files for each sample giving the SNP calls
            used
          pattern: "*.vcf"
  - versions:
      - versions.yml:
          type: file
          description: File containing software versions
          pattern: "versions.yml"
authors:
  - "@sppearce"
maintainers:
  - "@sppearce"
