fixed bugs in the annotation pipeline based on issues #61, #62 and #63.

PMBio · Apr 11, 2024 · fabcd11 · fabcd11
1 parent 101feb2
commit fabcd11
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Showing 3 changed files with 11 additions and 2 deletions.
diff --git 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
@@ -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
@@ -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
+    - git+https://github.com/gagneurlab/spliceai_rocksdb.git@v1.0.0