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

description

pattern

`ch_fastq`

Channel containing single or paired fastq files.

Structure: [ val(meta), [ path(fastq) ] ]

*.fastq.gz

`ch_snp_pt`

Channel containing the binary PT file with the SNPs to analyse. NGSCheckMate
provides one for human samples. Only the first element is used, so the meta
map identifies the SNP set, e.g. [ id:'sarscov2' ].

Structure: [ val(meta2), path(snp_pt) ]

*.pt

Output

name

description

pattern

`corr_matrix`

A text file containing the correlation matrix between each sample.

Structure: [ val(meta2), path(corr_matrix) ]

*corr_matrix.txt

`matched`

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

Structure: [ val(meta2), path(matched) ]

*matched.txt

`all`

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

Structure: [ val(meta2), path(all) ]

*all.txt

`vaf`

Per-sample text file containing the reference/alt allele depth for each SNP.

Structure: [ val(meta), path(vaf) ]

*.vaf

`pdf`

An optional pdf containing a dendrogram showing how the samples match up.

Structure: [ val(meta2), path(pdf) ]

*.pdf