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varfish-org · Jan 4, 2024 · 98204da · 98204da
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commit 98204da
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Showing 10 changed files with 13 additions and 11 deletions.
diff --git a/download_urls.yml b/download_urls.yml
@@ -91,12 +91,12 @@
 - url: ftp://ftp.clinicalgenome.org/ClinGen_gene_curation_list_GRCh37.tsv
 - url: ftp://ftp.clinicalgenome.org/ClinGen_gene_curation_list_GRCh38.tsv
 
-- url: https://storage.cloud.google.com/adult-gtex/bulk-gex/v8/rna-seq/GTEx_Analysis_v8_Annotations_SampleAttributesDS.txt
+- url: https://storage.googleapis.com/adult-gtex/annotations/v8/metadata-files/GTEx_Analysis_v8_Annotations_SampleAttributesDS.txt
   excerpt_strategy:
     strategy: no-excerpt
     count: null
 
-- url: https://storage.cloud.google.com/adult-gtex/bulk-gex/v8/rna-seq/GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_tpm.gct.gz
+- url: https://storage.googleapis.com/adult-gtex/bulk-gex/v8/rna-seq/GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_tpm.gct.gz
   excerpt_strategy:
     strategy: manual
     count: null

diff --git a/environment.yml b/environment.yml
@@ -41,7 +41,7 @@ dependencies:
   # Parallel (de)compression.
   - pigz
   # Varfish related
-  - annonars =0.32.0
+  - annonars =0.33.0
   - viguno =0.2.0
   - mehari =0.21.1
   - varfish-server-worker =0.10.2

diff --git a/...17-06-05_v8_RNASeQCv1.1.9_gene_tpm.gct.gz → ...17-06-05_v8_RNASeQCv1.1.9_gene_tpm.gct.gz b/...17-06-05_v8_RNASeQCv1.1.9_gene_tpm.gct.gz → ...17-06-05_v8_RNASeQCv1.1.9_gene_tpm.gct.gz
diff --git a/excerpt-data/4c4ffa6ddc180f40/url.txt b/excerpt-data/4c4ffa6ddc180f40/url.txt
diff --git a/...sis_v8_Annotations_SampleAttributesDS.txt → ...sis_v8_Annotations_SampleAttributesDS.txt b/...sis_v8_Annotations_SampleAttributesDS.txt → ...sis_v8_Annotations_SampleAttributesDS.txt
diff --git a/excerpt-data/4efb53cbe56f8290/url.txt b/excerpt-data/4efb53cbe56f8290/url.txt
diff --git a/excerpt-data/95e8d788836873e9/url.txt b/excerpt-data/95e8d788836873e9/url.txt
diff --git a/excerpt-data/d0a5951ccb4cd824/url.txt b/excerpt-data/d0a5951ccb4cd824/url.txt
diff --git a/rules/output/annonars/genes.smk b/rules/output/annonars/genes.smk
@@ -12,6 +12,7 @@ rule output_annonars_genes:  # -- build annonars genes RocksDB file
         ncbi="work/genes/entrez/{date}/gene_info.jsonl",
         omim="work/genes/omim/{v_hpo}+{date}/omim_diseases.tsv",
         orpha="work/genes/orphapacket/{v_orpha}+{date}/orpha_diseases.tsv",
+        panelapp="work/download/genes/panelapp/{date}/panelapp.jsonl",
         rcnv="work/genes/rcnv/2022/rcnv_collins_2022.tsv",
         shet="work/genes/shet/2019/shet_weghorn_2019.tsv",
         gtex="work/genes/annonars/gtex_v8/genes_tpm.jsonl.gz",
@@ -44,6 +45,7 @@ rule output_annonars_genes:  # -- build annonars genes RocksDB file
             --path-in-hgnc {input.hgnc} \
             --path-in-omim {input.omim} \
             --path-in-orpha {input.orpha} \
+            --path-in-panelapp {input.panelapp} \
             --path-in-ncbi {input.ncbi} \
             --path-in-rcnv {input.rcnv} \
             --path-in-shet {input.shet} \

diff --git a/rules/work/genes/gtex.smk b/rules/work/genes/gtex.smk
@@ -34,11 +34,11 @@ rule genes_gtex_v8_download:  # -- download GTex v8 gene expression data
         r"""
         wget --no-check-certificate \
             -O {output.attributes} \
-            https://storage.cloud.google.com/adult-gtex/bulk-gex/v8/rna-seq/GTEx_Analysis_v8_Annotations_SampleAttributesDS.txt
+            https://storage.googleapis.com/adult-gtex/annotations/v8/metadata-files/GTEx_Analysis_v8_Annotations_SampleAttributesDS.txt
 
         wget --no-check-certificate \
             -O {output.genes_tpm} \
-            https://storage.cloud.google.com/adult-gtex/bulk-gex/v8/rna-seq/GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_tpm.gct.gz
+            https://storage.googleapis.com/adult-gtex/bulk-gex/v8/rna-seq/GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_tpm.gct.gz
 
         md5sum {output.attributes} > {output.attributes_md5}
         md5sum {output.genes_tpm} > {output.genes_tpm_md5}