Add output directory argument

[rjcorb]

Purpose/implementation Section

What feature is being added or bug is being addressed?

Closes #156. This PR adds an output directory argument that allows users to specify where output of 01-annotate_variants_*_input.R and 04-filter_gene_annotations.R is written.

What was your approach?

• Added outdir argument when executing 01 and 04 scripts in run_autogvp.sh
• Added outdir to parsed parameters in 01 and 04 scripts

What GitHub issue does your pull request address?

156

Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.

Which areas should receive a particularly close look?

Please run on test data set, and specify different outdir folders to check that updated code works as expected. For example:

bash run_autogvp.sh --workflow="custom" \
--vcf=input/test_VEP.vcf \
--clinvar=input/clinvar.vcf.gz \
--intervar=input/test_VEP.hg38_multianno.txt.intervar \
--multianno=input/test_VEP.vcf.hg38_multianno.txt \
--autopvs1=input/test_autopvs1.txt \
--outdir=<out_dir>
--out="test_custom"

Is there anything that you want to discuss further?

No

Documentation Checklist

• [X] The function has examples to showcase the usage

[rjcorb]

Looks good to me! We'd just need to make sure we add this to the readme.

I just reviewed the README, and since we only show example usage for the full wrapper script execution (which already includes outdir argument), I think we are good.