Prepared by the eResearch Office, QUT.
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The Sarek workflow requires Nextflow to be installed in your account on the HPC. Find details on how to install and test Nextflow here and prepare a nextflow.config file and run a PBS pro submission script for Nextflow pipelines.
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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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