Annotate_Cohort_Upgrade

Dockerfile

@@ -1,7 +1,7 @@
 FROM australia-southeast1-docker.pkg.dev/cpg-common/images/cpg_hail_gcloud:0.2.137.cpg1-2
 
 ENV PYTHONDONTWRITEBYTECODE=1
-ENV VERSION=0.1.16
+ENV VERSION=0.1.17
 
 WORKDIR /cpg_seqr_loader
 

README.md

@@ -55,7 +55,7 @@ CPG-Flow workflows are operated entirely by defining input Cohorts (see [here](h
 ```bash
 analysis-runner \
     --skip-repo-checkout \
-    --image australia-southeast1-docker.pkg.dev/cpg-common/images/cpg-flow-seqr-loader:0.1.16 \
+    --image australia-southeast1-docker.pkg.dev/cpg-common/images/cpg-flow-seqr-loader:0.1.17 \
     --config src/cpg_seqr_loader/config_template.toml \
     --config cohorts.toml \  # containing the inputs_cohorts and sequencing_type
     --dataset seqr \
@@ -70,7 +70,7 @@ analysis-runner \
 ```bash
 analysis-runner \
     --skip-repo-checkout \
-    --image australia-southeast1-docker.pkg.dev/cpg-common/images/cpg-flow-seqr-loader:0.1.16 \
+    --image australia-southeast1-docker.pkg.dev/cpg-common/images/cpg-flow-seqr-loader:0.1.17 \
     --config src/cpg_seqr_loader/config_template.toml \
     --config cohorts.toml \  # containing the inputs_cohorts and sequencing_type
     --dataset seqr \

pyproject.toml

@@ -8,7 +8,7 @@ description='Seqr-Loader (gVCF-combiner) implemented in CPG-Flow'
 readme = "README.md"
 # currently cpg-flow is pinned to this version
 requires-python = ">=3.10,<3.12"
-version="0.1.16"
+version="0.1.17"
 license={"file" = "LICENSE"}
 classifiers=[
     'Environment :: Console',
@@ -120,7 +120,7 @@ hail = ["hail"]
 "src/cpg_seqr_loader/scripts/annotate_cohort.py" = ["E501"]
 
 [tool.bumpversion]
-current_version = "0.1.16"
+current_version = "0.1.17"
 parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)"
 serialize = ["{major}.{minor}.{patch}"]
 commit = true

src/cpg_seqr_loader/config_template.toml

@@ -24,7 +24,7 @@ driver_memory = "highmem"
 # string, e.g. "4Gi"
 driver_storage = "10Gi"
 # integer
-driver_cores = 2
+driver_cores = 8
 # highem, standard, or a string, e.g. "4Gi"
 worker_memory = "highmem"
 worker_cores = 1
@@ -49,7 +49,7 @@ worker_memory = "highmem"
 # highem, standard, or a string, e.g. "4Gi"
 driver_memory = "highmem"
 # integer
-driver_cores = 2
+driver_cores = 4
 
 [vcf_from_mt]
 # highem, standard, or a string, e.g. "4Gi"
@@ -84,7 +84,6 @@ liftover_38_to_37 = "gs://cpg-common-main/references/liftover/grch38_to_grch37.o
 seqr_clinvar = "gs://cpg-common-main/references/seqr/v0/clinvar.GRCh38.ht"
 seqr_combined_reference_data = "gs://cpg-common-main/references/seqr/v0/combined_reference_data_grch38.ht"
 vep_mount = "gs://cpg-common-main/references/vep/110/mount"
-
 # these are all related to VQSR
 axiom_poly_vcf = "gs://cpg-common-main/references/hg38/v0/Axiom_Exome_Plus.genotypes.all_populations.poly.hg38.vcf.gz"
 axiom_poly_vcf_index = "gs://cpg-common-main/references/hg38/v0/Axiom_Exome_Plus.genotypes.all_populations.poly.hg38.vcf.gz.tbi"

src/cpg_seqr_loader/scripts/annotate_cohort.py

@@ -238,6 +238,11 @@ def annotate_cohort(
         clinvar_data=clinvar_ht[mt.row_key],
         ref_data=ref_ht[mt.row_key],
     )
+    if avi_table := config.config_retrieve(['references', 'avi_table'], None):
+        refavis_ht = hl.read_table(avi_table)
+        loguru.logger.info('Annotating with refavis data')
+        mt = mt.annotate_rows(avis=(refavis_ht[mt.row_key].normalised_avis,))
+        mt.describe()
 
     # annotate all the gnomAD v4 fields in a separate function
     mt = annotate_gnomad4(mt)