Fixed issues found at runtime

Fixed small bugs found when testing code:

header in file is actually sample_id cram crai variants_tsv_bgz; renamed variables accordingly
crai is necessary for HaplotypeCaller; added back into necessary fields
set_gcloud_project was causing issues with my hail service account; removed
removed unused args num samples to process, sample to process
PrintReadsHeader does not exist in this version of gatk; removed
-T option doesn't work with this version of gatk; removed
fixed any missing backslashes in HaplotypeCaller command
removed disable_auto_index_creation_and_locking_when_reading_rods (not valid with this version of gatk)
fixed awk command -- chrom and pos are no longer cols 1 and 2 of variants_tsv_bgz

broadinstitute / ukbb_qc