# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
name: "bam_ngscheckmate"
description: Take a set of bam files and run NGSCheckMate to determine whether samples match with each other, using a set of SNPs.
keywords:
  - ngscheckmate
  - qc
  - bam
  - snp
components:
  - bcftools/mpileup
  - ngscheckmate/ncm
input:
  - meta1:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test' ]
  - bam:
      type: file
      description: BAM files for each sample
      pattern: "*.{bam}"
  - meta2:
      type: map
      description: |
        Groovy Map containing bed file information
        e.g. [ id:'sarscov2' ]
  - snp_bed:
      type: file
      description: BED file containing the SNPs to analyse. NGSCheckMate provides some default ones for hg19/hg38.
      pattern: "*.{bed}"
  - meta3:
      type: map
      description: |
        Groovy Map containing reference genome meta information
        e.g. [ id:'sarscov2' ]
  - fasta:
      type: file
      description: fasta file for the genome
      pattern: "*.{fasta}"
output:
  - pdf:
      type: file
      description: A pdf containing a dendrogram showing how the samples match up
      pattern: "*.{pdf}"
  - corr_matrix:
      type: file
      description: A text file containing the correlation matrix between each sample
      pattern: "*corr_matrix.txt"
  - matched:
      type: file
      description: A txt file containing only the samples that match with each other
      pattern: "*matched.txt"
  - all:
      type: file
      description: A txt file containing all the sample comparisons, whether they match or not
      pattern: "*all.txt"
  - vcf:
      type: file
      description: vcf files for each sample giving the SNP calls
      pattern: "*.vcf"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@SPPearce"
maintainers:
  - "@SPPearce"
