Human pipeline reference data generation tested and fixed#21

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pcharoentong wants to merge 10 commits intoroland-rad-lab:human-pipelinefrom pcharoentong:human-pipeline

+25-21

Commits on Aug 17, 2023

Clone the correct branch inside the dockerfile
charoentong
committed
Fixed dependencies. Without these the installation of r package devtools fails. Fixes issue roland-rad-lab#19
charoentong
committed
Fixed syntax error in script
charoentong
committed
Avoid running out of disk space in home directory
charoentong
committed
By deleting 00-All.vcf before creating 00-all.vcf, and not after, we avoid issues on file systems that are case insensitive, such as when docker mounts an NTFS volume from its windows host
charoentong
committed
Updated the gnomad bucket name
charoentong
committed
Updated dbNSFP version to 4.4a, since 4.1a is no longer available for download
charoentong
committed
Amazon link for dnNSFP is much faster than the softgenetics ftp server
charoentong
committed

Commits on Aug 18, 2023

Clean up the correct file
pcharoentong
authored

Commits on Aug 19, 2023

Fixed documentation of quality control parameter (it's actually -rq, not -qc)
charoentong
committed