bugfix

GC-HBOC · Nov 20, 2023 · bca30cb · bca30cb
1 parent e277a2f
commit bca30cb
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Showing 3 changed files with 13 additions and 13 deletions.
diff --git a/data/download_data.sh b/data/download_data.sh
@@ -470,17 +470,17 @@ wget https://www.omim.org/static/omim/data/mim2gene.txt
 
 
 ##Install COSMIC Cancer Mutation Census CMC  (you need a license, CMC tsv.gz file has to be downloaded manually from https://cancer.sanger.ac.uk/cmc/download)
-cd $dbs
-mkdir -p COSMIC
-cd COSMIC
-# HERE: we take a precalculated one using scripts from megSAP with correction script from alexander ott
-# /mnt/storage2/users/ahott1a1/projects/+analysis/230427_cosmic_converter/converted_corrected.vcf
-cp /mnt/storage2/users/ahott1a1/projects/+analysis/230427_cosmic_converter/converted_corrected.vcf .
-cat converted_corrected.vcf | $ngsbits/VcfLeftNormalize -stream -ref $grch38 | $ngsbits/VcfStreamSort | python3 $data/script/db_converter_cosmic.py > converted_corrected_collapsed.vcf
-rm converted_corrected.vcf
-mv converted_corrected_collapsed.vcf cosmic_cmc.vcf
-bgzip cosmic_cmc.vcf
-tabix -p vcf cosmic_cmc.vcf.gz
+#cd $dbs
+#mkdir -p COSMIC
+#cd COSMIC
+## HERE: we take a precalculated one using scripts from megSAP with correction script from alexander ott
+## /mnt/storage2/users/ahott1a1/projects/+analysis/230427_cosmic_converter/converted_corrected.vcf
+#cp /mnt/storage2/users/ahott1a1/projects/+analysis/230427_cosmic_converter/converted_corrected.vcf .
+#cat converted_corrected.vcf | $ngsbits/VcfLeftNormalize -stream -ref $grch38 | $ngsbits/VcfStreamSort | python3 $data/script/db_converter_cosmic.py > converted_corrected_collapsed.vcf
+#rm converted_corrected.vcf
+#mv converted_corrected_collapsed.vcf cosmic_cmc.vcf
+#bgzip cosmic_cmc.vcf
+#tabix -p vcf cosmic_cmc.vcf.gz
 
 
 

diff --git a/src/annotation_service/annotation_jobs/litvar2_job.py b/src/annotation_service/annotation_jobs/litvar2_job.py
@@ -35,7 +35,7 @@ def save_to_db(self, info, variant_id, conn):
         status_code = 0
         err_msg = ""
         if not self.job_config['do_litvar']:
-            return
+            return status_code, err_msg
 
         rsid_annotation_type_id = conn.get_most_recent_annotation_type_id("rsid")
         litvar_pmids = None

diff --git a/src/annotation_service/annotation_jobs/vep_job.py b/src/annotation_service/annotation_jobs/vep_job.py
@@ -49,7 +49,7 @@ def save_to_db(self, info, variant_id, conn):
             consequence_source = "ensembl"
 
         if csq_info == '' or csq_info is None:
-            return
+            return status_code, err_msg
 
         if self.job_config['insert_consequence']:
             conn.delete_variant_consequences(variant_id, is_refseq = self.refseq)