nf-core_modules/modules/ngscheckmate/ncm/meta.yml

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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: "doi:/10.1093/nar/gkx193"
licence: ['MIT']
input:
- 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}"
- snp_bed:
type: file
description: BED file containing the SNPs to analyse
pattern: "*.{bed}"
- fasta:
type: file
description: fasta file for the genome, only used in the bam mode
pattern: "*.{bed}"
output:
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- 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"
- vcfs:
type: file
description: If ran in bam mode, vcf files for each sample giving the SNP calls
pattern: "*.vcf"
authors:
- "@sppearce"