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feat: use latest VRS Python annotator API + return logs #8

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feat: use latest VRS Python annotator API + return logs #8

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4 changes: 2 additions & 2 deletions containers/base/Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -10,8 +10,8 @@ RUN cd ~ && \
make install && \
export BCFTOOLS_PLUGINS=~/bcftools/plugins/

RUN pip install ga4gh.vrs[extras]==2.0.0a7 biocommons.seqrepo
RUN pip install ga4gh.vrs[extras]==2.0.0a11 biocommons.seqrepo

RUN sudo apt-get update && sudo apt-get install -y rsync

CMD ["/bin/bash"]
CMD ["/bin/bash"]
12 changes: 6 additions & 6 deletions vrs-annotator.wdl
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Expand Up @@ -4,7 +4,7 @@ version 1.0
workflow VRSAnnotator {
input {
File input_vcf_path
String output_vcf_name
String output_vcf_name
File seqrepo_tarball
Boolean compute_for_ref = true
Boolean compute_vrs_attributes = true
Expand Down Expand Up @@ -67,27 +67,27 @@ task annotate {
else
REF_FLAG="--skip_ref"
fi

if ~{compute_vrs_attributes}; then
VRS_ATTRIBUTES_FLAG="--vrs_attributes"
else
VRS_ATTRIBUTES_FLAG=""
fi

# annotate and index vcf
python -m ga4gh.vrs.extras.vcf_annotation \
--vcf_in ~{input_vcf_path} \
vrs-annotate vcf ~{input_vcf_path} \
--vcf_out ~{output_vcf_name} \
--seqrepo_root_dir $SEQREPO_DIR/latest \
--assembly ~{genome_assembly} \
$REF_FLAG \
$VRS_ATTRIBUTES_FLAG

bcftools index -t ~{output_vcf_name}
>>>

output {
File annotated_vcf = "~{output_vcf_name}"
File annotated_vcf_index = "~{output_vcf_name}.tbi"
File vrs_annotation_log = "vrs-annotate.log"
}
}
}