nf-NGSCheckMate

Nextflow workflow running NGSCheckMate

NGSCheckMate is a software package for identifying next generation sequencing (NGS) data files from the same individual. More details can be found on its official repository.

Input Data

Sample Sheet CSV

This workflow is designed to analyze WGS data provided as paired-end FASTQ files, with one pair per sample.

The inputs files should be specified with a sample sheet CSV with the format:

sample,fastq_1,fastq_2
sampleA,/path/to/sampleA.R1.fastq.gz,/path/to/sampleA.R2.fastq.gz
sampleB,/path/to/sampleB.R1.fastq.gz,/path/to/sampleB.R2.fastq.gz
sampleC,/path/to/sampleC.R1.fastq.gz,/path/to/sampleC.R2.fastq.gz

The location of the sample sheet should be supplied with the parameter paired_fastq_samplesheet.

Wildcard Pattern

An alternate approach for specifying input files is with a wildcard pattern which indicates the pairs of files which belong to the same sample. The parameter for that pattern is paired_fastq_path.

For example, the files listed in the sample sheet CSV shown above could be captured with the pattern /path/to/*.R{1,2}.fastq.gz. The two elements of the wildcard pattern which should be used are *, which represents the variable part of the filename that matches the sample ID, and {1,2}, which indicates the position which contains 1 in the read 1 file name and 2 in the read 2 file name.

Parameters

• paired_fastq_samplesheet: Sample sheet CSV indicating the location of all input files (cannot use with --paired_fastq_path)
• paired_fastq_path: Sample sheet CSV indicating the location of all input files (cannot use with --paired_fastq_samplesheet)
• outdir: Location for output file (NGSCheckMate.results.csv) to be written
• ref: Binary pattern file used as a reference (default: https://github.com/parklab/NGSCheckMate/raw/master/SNP/SNP.pt)

nextflow run

nextflow run nf-ngscheckmate/main.nf  --outdir sr-mates --paired_fastq_samplesheet samples_paired_ngscheck.txt  -profile kutral