fastq_ngscheckmate

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

ngscheckmateqcfastqsnp

https://github.com/nf-core/modules/[...]/subworkflows/nf-core/fastq_ngscheckmate

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