From e1c259787bb966da5cca8b6f92fffe48b62749f8 Mon Sep 17 00:00:00 2001
From: Manuel Holtgrewe <manuel.holtgrewe@bih-charite.de>
Date: Wed, 22 Nov 2023 08:32:16 +0100
Subject: [PATCH] feat: adding DECIPHER HI to annonars genes

---
 environment.yml                 | 2 +-
 rules/output/annonars/genes.smk | 7 +++----
 2 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/environment.yml b/environment.yml
index ae69a76..a74e265 100644
--- a/environment.yml
+++ b/environment.yml
@@ -41,7 +41,7 @@ dependencies:
   # Parallel (de)compression.
   - pigz
   # Varfish related
-  - annonars =0.27.0
+  - annonars =0.28.0
   - viguno =0.1.6
   - mehari =0.6.2
   - varfish-server-worker =0.10.1
diff --git a/rules/output/annonars/genes.smk b/rules/output/annonars/genes.smk
index 8a40cdf..622cd6c 100644
--- a/rules/output/annonars/genes.smk
+++ b/rules/output/annonars/genes.smk
@@ -16,6 +16,7 @@ rule output_annonars_genes:  # -- build annonars genes RocksDB file
         shet="work/genes/shet/2019/shet_weghorn_2019.tsv",
         gtex="work/genes/annonars/gtex_v8/genes_tpm.jsonl.gz",
         domino="work/genes/domino/20190219/domino.tsv",
+        decipher_hi="work/genes/decipher/v3/decipher_hi_prediction.tsv.gz",
     output:
         rocksdb_identity=(
             "output/full/annonars/genes-{v_acmg_sf}+{v_gnomad_constraints}+{v_dbnsfp}+{v_hpo}+{v_orpha}+{date}+{v_annonars}/"
@@ -36,14 +37,11 @@ rule output_annonars_genes:  # -- build annonars genes RocksDB file
         export TMPDIR=$(mktemp -d)
         trap "rm -rf $TMPDIR" EXIT
 
-        tail -n +4 {input.clingen} > $TMPDIR/clingen.csv
-
         annonars gene import \
             --path-out-rocksdb $(dirname {output.rocksdb_identity}) \
             --path-in-acmg {input.acmg_sf} \
             --path-in-clingen-37 {input.clingen_37} \
             --path-in-clingen-38 {input.clingen_38} \
-            --path-in-clingen $TMPDIR/clingen.csv \
             --path-in-gnomad-constraints {input.gnomad_constraints} \
             --path-in-dbnsfp {input.dbnsfp} \
             --path-in-hgnc {input.hgnc} \
@@ -53,7 +51,8 @@ rule output_annonars_genes:  # -- build annonars genes RocksDB file
             --path-in-rcnv {input.rcnv} \
             --path-in-shet {input.shet} \
             --path-in-gtex {input.gtex} \
-            --path-in-domino {input.domino}
+            --path-in-domino {input.domino} \
+            --path-in-decipher-hi {input.decipher_hi}
 
         varfish-db-downloader tpl \
             --template rules/output/annonars/genes.spec.yaml \