Squashed commit of the following:

commit ae5c83e
Author: Marcel Mück <mueckm1@gmail.com>
Date:   Mon Apr 15 11:01:03 2024 +0200

    fixed bugs in the annotation pipeline based on issues #61, #62 and #63. (#64)

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

    * fixup! Format Python code with psf/black pull_request

    ---------

    Co-authored-by: “Marcel-Mueck” <“mueckm1@gmail.com”>
    Co-authored-by: PMBio <PMBio@users.noreply.github.com>

commit 101feb2
Author: Marcel Mück <mueckm1@gmail.com>
Date:   Tue Apr 9 11:56:54 2024 +0200

    Annotations new features (#54)

    * added all changes from annotation-speedups branch

    * added gtf and genotype mock file for github tests

    * Delete example/annotations/preprocessing_workdir/preprocessed directory

    * Update annotation_colnames_filling_values.yaml

    * Corrected fill values for maf columns

    * Changed protein_id merging and exon distance filtering, s.t. no annotations are dropped

    * included rulegraph instead dag

    * based on  suggestions from @endast

    * added version info for rockdb.yaml file

    * updated rulegraph

    Updated Documentation

    corrected nonfunctional links

    * added support for X/Y chromosomes, removed dependency on pvcf file

    * excluded mkl version 2024.1.0  since it is crashing pytorch(pytorch/pytorch#123097)

    * changed way file stems are assumed to include 'double ending' on input files.

    * removed unused lines, removed pvcf from config file

    * changed if statement for gene_id_file

    ---------

    Co-authored-by: “Marcel-Mueck” <“mueckm1@gmail.com”>
    Co-authored-by: PMBio <PMBio@users.noreply.github.com>

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(

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(

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