Purpose/implementation Section

What feature is being added or bug is being addressed?

Closes #182. This PR adds conditionals to ensure that all necessary ClinVar files are downloaded prior to running AutoGVP. A base directory was also defined and file paths were adjusted such that run_autogvp.sh can now be run from any directory.

What was your approach?

Added two conditional statements to run_autogvp.sh. The first downloads variant_summary.txt.gz and submission_summary.txt.gz from ClinVar database if they are not already downloaded, and the second runs select-clinVar-submissions.R if ClinVar-selected-submissions.tsv is not present.
Added a BASEDIR variable that is set to the root directory of the repo

What GitHub issue does your pull request address?

182

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

Which areas should receive a particularly close look?

To check that input files are downloaded when they are not present, please remove files variant_summary.txt.gz, submission_summary.txt.gz, and ClinVar-selected-submissions.tsv from working directory, and then run autogvp from root directory:

bash run_autogvp.sh --workflow="cavatica" \
--vcf=data/test_pbta.single.vqsr.filtered.vep_105.vcf \
--filter_criteria='FORMAT/DP>=10 (FORMAT/AD[0:1-])/(FORMAT/DP)>=0.2 (gnomad_3_1_1_AF_non_cancer<0.001|gnomad_3_1_1_AF_non_cancer=".")' \
--intervar=data/test_pbta.hg38_multianno.txt.intervar \
--multianno=data/test_pbta.hg38_multianno.txt \
--autopvs1=data/test_pbta.autopvs1.tsv \
--outdir=results \
--out="test_pbta"

Is there anything that you want to discuss further?

This can also be tested to run from different directories, but the input file paths in the above command would need to be changed accordingly.

Documentation Checklist

[X] The function has examples to showcase the usage

diskin-lab-chop / AutoGVP

Update wrapper script conditionals and base directory #185