How to run WGS-Seek

Guide

• ./wgs-seek - Starts a next nextflow run Supports runs from Fastq and either Tumor-Normal or Tumor-only Sequencing

Running Nextflow

Multiple options required for running

Code

./wgs-seek --fastq "Samples/Sample_R{1,2}.fastq.gz" --output 'B2' --sample_sheet sample.tsv --paired T --profile biowulf

Arguments

Input selection can either be
--fastq 1) A wildcard expansion of Fastq files "Samples/Sample_*R{1,2}.fastq.gz" which finds all Samples in the directory with the head Sample
OR
--filelist 2a) A tab separated file with 3 columns Sample Name, Fastq1 Full path, Fastq2 Full Path if using fastq files or 2b) A tab separated file with 2 columns Sample Name, BAM file path

--output - Output Directory

--sample_sheet- Tab separated file for Normal and Tumor delination with a header for "Normal" and "Tumor"

--profile Biowulf or Local Run

--resume Resume previous nextflow run

--submit- Submit job to Biowulf?

--paired- Are Samples paired Tumor-Normal