Re-adjust user's project folder file path based on user's preference

[nluu1]

Based on the group discussion today (08/04/23):

• We need to adjust the /media/volume/sdb (with no end slash) into a variable, as discussed $4
• All the scripts have to be updated with the variable for this file path.

[nluu1]

@LloydJonesIII Based on our brief discussion, can you adjust the following path variable in the annotation_config.sh:

REFDIR="/media/volume/sdb/$1/assembly/reference/ncbi_dataset/data"

RESULT_PATH="/media/volume/sdb/$1/assembly/results"

RESOURCE_PATH="/media/volume/sdb/$1/assembly/resources"

SNPEFF_PATH="/media/volume/sdb/$1/assembly/resources/SnpEff"

with /media/volume/sdb into $2, so the variables become:

REFDIR="$2/$1/assembly/reference/ncbi_dataset/data"

RESULT_PATH="$2/$1/assembly/results"

RESOURCE_PATH="$2/$1/assembly/resources"

SNPEFF_PATH="$2/$1/assembly/resources/SnpEff"

[nluu1]

Seems like the VCF Generator automation works with @LloydJonesIII's bigrun2. I'm closing this issue as of 08/15/2023.