Update repo directory structure

[rjcorb]

Purpose/implementation Section

What feature is being added or bug is being addressed?

Closes #183. This PR creates the following repo folders:

• data/ for all test files and input data (clinvar db files, output_colnames.tsv); files were moved from AutoGVP/input/
• docker_scripts/ for install shell scripts required to build docker image; files were moved from scripts/
• scripts/ for all shell and R scripts other than wrapper script; files were moved from AutoGVP/

Additionally, the wrapper script run_autogvp.sh was moved to the root directory.

What was your approach?

• Created new directories and transferred files to appropriate directories.
• removed outdated scripts and test files
• Updated file paths in relevant shell and R scripts
• Updated README to reflect new file paths

What GitHub issue does your pull request address?

183

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

Which areas should receive a particularly close look?

Please review new directory structure--any feedback on naming of folders or placement of files is welcome. Also please run the following commands from root directory to ensure that all scripts still run as expected:

download clinvar db files:

bash scripts/download_db_files.sh

run select-ClinVar-submissions.R:

Rscript scripts/select-clinVar-submissions.R --variant_summary data/variant_summary.txt.gz --submission_summary data/submission_summary.txt.gz

cavatica autogvp:

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"

custom autogvp:

bash run_autogvp.sh --workflow="custom" \
--vcf=data/test_VEP.vcf \
--clinvar=data/clinvar.vcf.gz \
--intervar=data/test_VEP.hg38_multianno.txt.intervar \
--multianno=data/test_VEP.vcf.hg38_multianno.txt \
--autopvs1=data/test_autopvs1.txt \
--outdir=results \
--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]

@jharenza I've updated the .gitignore and pushed the updated dockerfile