re-add pathogenic VCF stubs

.bumpversion.cfg

@@ -4,3 +4,5 @@ commit = True
 tag = False
 
 [bumpversion:file:setup.py]
+
+[bumpversion:file:Dockerfile]

Dockerfile

@@ -15,4 +15,4 @@ RUN apt update && apt install -y \
     rm -r /var/lib/apt/lists/* && \
     rm -r /var/cache/apt/*
 
-RUN pip install --no-cache-dir git+https://github.com/populationgenomics/automated-interpretation-pipeline.git@${RELEASE}
+RUN pip install --no-cache-dir git+https://github.com/populationgenomics/ClinvArbitration.git@${RELEASE}

example_script.sh

@@ -3,7 +3,7 @@
 set -ex
 
 # create a docker image from this repository
-docker build --platform linux/arm64/v8 -t hail_clinvar:example --platform linux/amd64 .
+docker build --platform linux/arm64/v8 -t clinvarbitration:example --platform linux/amd64 .
 
 # make local copies of the NCBI data files required as input using wget
 # create a directory called data, if one doesn't already exist
@@ -14,7 +14,7 @@ fi
 #wget -O data/submission_summary.txt.gz https://ftp.ncbi.nlm.nih.gov/pub/clinvar/tab_delimited/submission_summary.txt.gz
 
 # run the docker image to generate the summarised output
-docker run -v "$(pwd)/data":/data hail_clinvar:example \
+docker run -v "$(pwd)/data":/data clinvarbitration:example \
     resummary -v "/data/variant_summary.txt.gz" -s "/data/submission_summary.txt.gz" -o "/data/clinvar_summary" --minimal
 
 # upon completion, this will have generated files in the data directory:
@@ -26,8 +26,8 @@ docker run -v "$(pwd)/data":/data hail_clinvar:example \
 ## This is where you should run VEP on data/clinvar_summary.vcf.bgz, with protein consequence annotation per transcript
 ## Let's imagine you did that, and the result is in data/pathogenic_annotated.vcf.bgz
 ## I've enclosed a 10-variant example of this, as annotated by https://www.ensembl.org/Homo_sapiens/Tools/VEP
-#docker run --platform linux/amd64 -v "$(pwd)/data":/data hail_clinvar:example \
-#    /bin/bash -c "python3 /clinvarbitration/clinvar_by_codon_from_vcf.py -i /data/pathogenic_annotated.vcf.bgz -o /data/pm5"
+#docker run --platform linux/amd64 -v "$(pwd)/data":/data clinvarbitration:example \
+#    /bin/bash -c "python3 /clinvarbitration/clinvar_by_codon.py -i /data/pathogenic_annotated.vcf.bgz -o /data/pm5"
 
 # upon completion, this will generate files in the data directory:
 # - data/pm5.json - a JSON file containing the PM5 results, one JSON object per line