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Data requirements change depending on the step you start with. Check the Sarek documentation for details.nextflow run nf-core/sarek -profile test,singularity

Run test

#run test
nextflow run nf-core/sarek -profile test,singularity

#resume
nextflow run nf-core/sarek -profile test,singularity -resume 

Preparing Data

Starting the Sarek workflow at the “mapping” step requires paired fastq files (See Sarek documentation for details). You need to create a suitable TAB separated text file that will be the input for the workflow. Mapping requires the following columns

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In the folder you have created for this run create launch.pbs

#!/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 option to run Sark (define parameters in the command)

#!/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 -profile singularity \
  --input sample.tsv -name GRCh38_FBS1_LNCAP \
  --genome GRCh38 --tools HaplotypeCaller,snpEff,VEP \
  --generate_gvcf

Submitting the job

Once you have created the folder for the run, the input.tsv file, nextflow.config and launch.pbs you are ready to submit.

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