Still under development!
bash deploy_hopper.sh (to /fs1/pipelines/twist-brca/)
To run nextflow with singularity on hopper you need first module load.
module load Java singularity nextflow
the run command should look like this.
nextflow run main.nf --csv input.csv -with-singularity /fs1/resources/containers/container_twist-brca.sif -resume --reads 1,1,0 --manta --melt
needs to have the following headers
clarity_sample_id,id,assay,sex,diagnosis,phenotype,group,clarity_pool_id,platform,read1,read2
example-files can be located /fs1/pipelines/twist-brca/test_files/ any csv that should work.
Melt will fail if it cannot find any mobile elements at all. As such, errors from this process is ignored and no vcf will be produced.