Prepared by the eResearch Office, QUT.
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subject sex status sample lane fastq1 fastq2
Example input 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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params {
input = 'inputsample.tsv'
genome = 'GRCh38'
tools = 'HaplotypeCaller,mpileup,snpEFF,VEP,CNVkit'
}
tower {
accessToken = 'your tower token'
endpoint = 'https://nftower.qut.edu.au/api'
enabled = true
} |
For this, you have to put in your tower token. You will be assigned a token once you sign in via https://nftower.qut.edu.au/api
With this file in place, the command to run the pipeline is
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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 |
Alternative An alternative option to run Sark Sarek (define parameters in the command)
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