Prepared by the eResearch Office, QUT.
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This page provides a guide to QUT users to run the nf-core/sarek workflow on the QUT HPC.
Installed conda3 or miniconda3 ( https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html )
Further details on the workflow can be found at:
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subject sex status sample lane fastq1 fastq2
Example sample.tsv
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Subject01 XX 0 Sample01 1 /work/group/data/subject01-sample01_R1.fastq.gz /work/group/data/subject01-sample01_R2.fastq.gz Subject02 XX 0 Sample01 1 /work/group/data/subject02-sample01_R1.fastq.gz /work/group/data/subject02-sample01_R2.fastq.gz |
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nextflow run /nf-cire/sarek -profile singularity --input 'input.tsv' --genome 'GRCh38' --tools 'HaplotypeCaller,mpileup,snpEFF' |
Or, create a nextflow.config file to store the options in a different place.
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In the folder you have created for this run create launch.pbs
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#!/bin/bash -l #PBS -N MySarekRun #PBS -l walltime=168:00:00 #PBS -l select=1:ncpus=1:mem=5gb cd $PBS_O_WORKDIR NXF_OPTS='-Xms1g -Xmx4g' module load java nextflow run nf-core/sarek |
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