Running GVCF Only

To run GVCF only, simply add the –gvcf_only parameter

Important note: if the pipeline run starts from the GVCF workflow, the --inputdir must point to the .sorted.dup.pf.bam files directory, which is one of the final outputs if the QC workflow.

nextflow run main.nf \
-profile sge,apptainer \
--inputdir path/input_directory_bam \
--outputdir path/output_directory \
--gvcf_only true