You cannot select more than 25 topics
Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
65 lines
1.9 KiB
YAML
65 lines
1.9 KiB
YAML
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"
|