diff --git a/data/download_data.sh b/data/download_data.sh index 609bc971..4620d8af 100755 --- 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 index d3b369c1..14a9e780 100644 --- 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 index 98155048..aa287d8b 100644 --- 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)