clinical-genomics-lund / nextflow_twist-brca

Nextflow pipeline for TWIST-BRCA

Nextflow pipeline for TWIST-Ärftlig Cancer

Still under development!

Deploy

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

CSV-file

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.

Known Issues

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.

nextflow_twist-brca's Issues

hg38

Switch to hg38 before validation!