Description

Take a set of fastq files and run NGSCheckMate to determine whether samples match with each other, using a set of SNPs.

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:'test' ]

fastq (file)

Single or pair of fastq files

*.{fastq.gz}

meta2 (map)

Groovy Map containing snp_pt file information
e.g. [ id:‘sarscov2’ ]

snp_bed (file)

Binary PT file containing the SNPs to analyse. NGSCheckMate provides one for human samples.

*.{bed}

Output

Name (Type)
Description
Pattern

pdf (file)

A pdf containing a dendrogram showing how the samples match up

*.{pdf}

corr_matrix (file)

A text file containing the correlation matrix between each sample

*corr_matrix.txt

matched (file)

A txt file containing only the samples that match with each other

*matched.txt

all (file)

A txt file containing all the sample comparisons, whether they match or not

*all.txt

vcf (file)

vcf files for each sample giving the SNP calls

*.vcf

versions (file)

File containing software versions

versions.yml