Updated scripts to handle IGV automated snapshot generation

.gitignore

assets/trio_whole_exome_bcbio_template.yaml

bin/convert_DEC_to_v10.py

bin/extract_solo_FAM_PRO_ID.py

bin/extract_trio_FAM_PRO_ID.py

bin/filter_LQ_GT.py

bin/generate_DEC_IGV_scripts.py

bin/get_cov_output.py

lib/PipelineException.groovy

main.nf

nextflow.config

pipeline/cram_compression.nf

pipeline/validation.nf

pipeline/var_calling.nf

pipeline/variant_prioritisation.nf

tests/assets/input_data/ped_files/batch_1.ped

tests/assets/input_data/ped_files/giab_test_trios.ped

.../input_data/sample_sheets/DECIPHER_INTERNAL_IDs_stubs.txt

tests/assets/input_data/sample_sheets/batch_1.tsv

tests/assets/input_data/sample_sheets/giab_test_trios.tsv