add sample id column to final output

[rjcorb]

Purpose/implementation Section

What feature is being added or bug is being addressed?

closes #162. This PR updates code to include a sample_id column in final AutoGVP output

What was your approach?

The --out argument supplied when running run_autogvp.sh is added as a column in final output.

What GitHub issue does your pull request address?

162

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 pbta and custom files, and confirm that sample_id column is present in output

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=../results \
--out="test_custom"

bash run_autogvp.sh --workflow="cavatica" \
--vcf=input/test_pbta.single.vqsr.filtered.vep_105.vcf \
--filter_criteria='INFO/AF>=0.2 INFO/DP>=15 (gnomad_3_1_1_AF_non_cancer<0.01|gnomad_3_1_1_AF_non_cancer=".")' \
--intervar=input/test_pbta.hg38_multianno.txt.intervar \
--multianno=input/test_pbta.hg38_multianno.txt \
--autopvs1=input/test_pbta.autopvs1.tsv \
--outdir=../results \
--out="test_pbta"

Is there anything that you want to discuss further?

No

Documentation Checklist

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