From 23e7de72adc775617307bdab3a4415dd0db69e9b Mon Sep 17 00:00:00 2001
From: Manuel Holtgrewe <manuel.holtgrewe@bihealth.de>
Date: Wed, 19 Jun 2024 12:27:55 +0200
Subject: [PATCH] cleanup

---
 Snakefile                             |  5 ----
 rules/output/worker/genes_regions.smk | 35 ---------------------------
 2 files changed, 40 deletions(-)
 delete mode 100644 rules/output/worker/genes_regions.smk

diff --git a/Snakefile b/Snakefile
index 22b880d..81b6599 100644
--- a/Snakefile
+++ b/Snakefile
@@ -180,10 +180,6 @@ rule all:
         # ----- genes
         f"output/full/annonars/genes-{DV.acmg_sf}+{DV.gnomad_constraints}+{DV.dbnsfp}+{DV.hpo}+{DV.today}+{PV.annonars}/rocksdb/IDENTITY",
         # -- worker data
-        f"output/full/worker/genes-regions-grch37-{DV.refseq_37}+{PV.worker}/refseq_genes.bin",
-        f"output/full/worker/genes-regions-grch37-{DV.ensembl_37}+{PV.worker}/ensembl_genes.bin",
-        f"output/full/worker/genes-regions-grch38-{DV.refseq_38}+{PV.worker}/refseq_genes.bin",
-        f"output/full/worker/genes-regions-grch38-{DV.ensembl_38}+{PV.worker}/ensembl_genes.bin",
         f"output/full/worker/genes-xlink-{DV.today}+{PV.worker}/genes-xlink.bin",
         f"output/full/worker/acmg-sf-{DV.acmg_sf}+{PV.worker}/acmg_sf.tsv",
         f"output/full/worker/mim2gene-{DV.today}+{PV.worker}/mim2gene.tsv",
@@ -411,7 +407,6 @@ include: "rules/output/annonars/regions.smk"
 # ---- worker
 include: "rules/output/worker/patho_mms.smk"
 include: "rules/output/worker/clinvar.smk"
-include: "rules/output/worker/genes_regions.smk"
 include: "rules/output/worker/hgnc.smk"
 include: "rules/output/worker/acmg.smk"
 include: "rules/output/worker/mim2gene.smk"
diff --git a/rules/output/worker/genes_regions.smk b/rules/output/worker/genes_regions.smk
deleted file mode 100644
index 03685c3..0000000
--- a/rules/output/worker/genes_regions.smk
+++ /dev/null
@@ -1,35 +0,0 @@
-## Convert gene regions to binary for worker.
-
-
-def input_genes_regions_worker_convert(wildcards):
-    """Input function for rule genes_regions_worker_convert."""
-    return {
-        "bed": f"work/annos/{wildcards.genome_release}/features/{wildcards.source}/{wildcards.version}/{wildcards.source}_genes.bed.gz",
-    }
-
-
-rule genes_regions_worker_convert:
-    input:
-        unpack(input_genes_regions_worker_convert),
-    output:
-        bin=f"output/full/worker/genes-regions-{{genome_release}}-{{version}}+{PV.worker}/{{source}}_genes.bin",
-        spec_yaml=f"output/full/worker/genes-regions-{{genome_release}}-{{version}}+{PV.worker}/{{source}}_genes.spec.yaml",
-    shell:
-        r"""
-        varfish-server-worker \
-            db to-bin \
-            --input-type gene-region \
-            --path-input {input.bed} \
-            --path-output {output.bin}
-
-        varfish-db-downloader tpl \
-            --template rules/output/worker/{wildcards.source}_genes.spec.yaml \
-            --value today={TODAY} \
-            --value genome_release={wildcards.genome_release} \
-            \
-            --value version={wildcards.version} \
-            \
-            --value v_worker={PV.worker} \
-            --value v_downloader={PV.downloader} \
-        > {output.spec_yaml}
-        """