diff --git a/deeprvat/annotations/annotations.py b/deeprvat/annotations/annotations.py index 53c1b295..ee534712 100644 --- a/deeprvat/annotations/annotations.py +++ b/deeprvat/annotations/annotations.py @@ -1899,6 +1899,15 @@ def process_vep( "Consequence_inframe_deletion", "Consequence_missense_variant", "Consequence_non_coding_transcript_variant", + "Consequence_TFBS_amplification", + "Consequence_coding_transcript_variant", + "Consequence_feature_elongation", + "Consequence_feature_truncation", + "Consequence_regulatory_region_ablation", + "Consequence_regulatory_region_amplification", + "Consequence_sequence_variant", + "Consequence_transcript_ablation", + "Consequence_transcript_amplification", ] all_consequences = list(set(all_consequences)) mask = pd.DataFrame( diff --git a/pipelines/resources/absplice_download.snakefile b/pipelines/resources/absplice_download.snakefile index 2ccb8483..e92705fd 100644 --- a/pipelines/resources/absplice_download.snakefile +++ b/pipelines/resources/absplice_download.snakefile @@ -126,7 +126,7 @@ if absplice_main_conf['use_rocksdb'] == True: conda: f"./environment_spliceai_rocksdb.yaml" output: - spliceai_rocksdb = Path(absplice_download_dir) / directory(config_download['spliceai_rocksdb'][genome]) + spliceai_rocksdb = directory(Path(absplice_download_dir) / config_download['spliceai_rocksdb'][genome]) shell: "spliceai_rocksdb_download --version {params.version} --db_path {output.spliceai_rocksdb} --chromosome {wildcards.chromosome}" list_outputs.append( diff --git a/pipelines/resources/environment_spliceai_rocksdb.yaml b/pipelines/resources/environment_spliceai_rocksdb.yaml index f59f3261..93e4f879 100755 --- a/pipelines/resources/environment_spliceai_rocksdb.yaml +++ b/pipelines/resources/environment_spliceai_rocksdb.yaml @@ -19,4 +19,4 @@ dependencies: - bioconda::spliceai==1.3.1 - bioconda::cyvcf2==0.30.16 - pip: - - git+https://github.com/gagneurlab/spliceai_rocksdb.git@0.0.1 \ No newline at end of file + - git+https://github.com/gagneurlab/spliceai_rocksdb.git@v1.0.0 \ No newline at end of file