diff --git a/pipelines/annotations.snakefile b/pipelines/annotations.snakefile
index c73b42d2..d2a42f64 100644
--- a/pipelines/annotations.snakefile
+++ b/pipelines/annotations.snakefile
@@ -4,6 +4,7 @@ from pathlib import Path
 
 configfile: "config/deeprvat_annotation_config.yaml"
 
+
 # init general
 
 species = config.get("species") or "homo_sapiens"
@@ -26,8 +27,12 @@ saved_deepripe_models_path = (
 merge_nthreads = int(config.get("merge_nthreads") or 64)
 
 # If modules are used we load them here
-load_bfc = " ".join([config["bcftools_load_cmd"], "&&" if config["bcftools_load_cmd"] else ""])
-load_hts = " ".join([config["htslib_load_cmd"], "&&" if config["htslib_load_cmd"] else ""])
+load_bfc = " ".join(
+    [config["bcftools_load_cmd"], "&&" if config["bcftools_load_cmd"] else ""]
+)
+load_hts = " ".join(
+    [config["htslib_load_cmd"], "&&" if config["htslib_load_cmd"] else ""]
+)
 load_perl = " ".join([config["perl_load_cmd"], "&&" if config["perl_load_cmd"] else ""])
 load_vep = " ".join([config["vep_load_cmd"], "&&" if config["vep_load_cmd"] else ""])
 
@@ -53,7 +58,7 @@ vep_cache_dir = Path(config.get("vep_cache_dir")) or vep_source_dir / "cache"
 vep_plugin_dir = Path(config.get("vep_plugin_dir")) or vep_source_dir / "Plugin"
 vep_input_format = config.get("vep_input_format") or "vcf"
 vep_nfork = int(config.get("vep_nfork") or 5)
-af_mode= config.get("af_mode") or "af"
+af_mode = config.get("af_mode") or "af"
 
 # init plugIns
 spliceAI_snv_file = config["spliceAI_snv_file"]
@@ -72,11 +77,11 @@ pvcf_blocks_df = pd.read_csv(
 absplice_repo_dir = Path(config["absplice_repo_dir"])
 n_cores_absplice = int(config.get("n_cores_absplice") or 4)
 ncores_merge_absplice = int(config.get("n_cores_merge_absplice") or 64)
-#init deepripe
+# init deepripe
 n_jobs_deepripe = int(config.get("n_jobs_deepripe") or 8)
 # init kipoi-veff2
 kipoi_repo_dir = Path(config["kipoiveff_repo_dir"])
-ncores_addis  = int(config.get("n_jobs_addids") or 32)
+ncores_addis = int(config.get("n_jobs_addids") or 32)
 # Filter out which chromosomes to work with
 pvcf_blocks_df = pvcf_blocks_df[
     pvcf_blocks_df["Chromosome"].isin([str(c) for c in included_chromosomes])
@@ -103,16 +108,19 @@ rule all:
 rule aggregate_and_merge_absplice:
     input:
         abscore_files=expand(
-            [anno_tmp_dir / "absplice" / (source_variant_file_pattern + "_AbSplice_DNA.csv")],
+            [
+                anno_tmp_dir
+                / "absplice"
+                / (source_variant_file_pattern + "_AbSplice_DNA.csv")
+            ],
             zip,
             chr=chromosomes,
             block=block,
         ),
-        current_annotation_file=anno_dir / "vep_deepripe_deepsea.parquet"
+        current_annotation_file=anno_dir / "vep_deepripe_deepsea.parquet",
     output:
         annotations=anno_dir / "current_annotations_absplice.parquet",
-        scores=anno_tmp_dir / "abSplice_score_file.parquet"
-
+        scores=anno_tmp_dir / "abSplice_score_file.parquet",
     shell:
         " ".join(
             [
@@ -123,10 +131,9 @@ rule aggregate_and_merge_absplice:
                 str(anno_tmp_dir / "absplice"),
                 "{output.annotations}",
                 "{output.scores}",
-                f"{ncores_merge_absplice}"
-            ])
-
-
+                f"{ncores_merge_absplice}",
+            ]
+        )
 
 
 rule merge_deepsea_pcas:
@@ -134,7 +141,7 @@ rule merge_deepsea_pcas:
         annotations=anno_dir / "vep_deepripe.parquet",
         deepsea_pcas=anno_dir / "deepSea_pca" / "deepsea_pca.parquet",
     output:
-        anno_dir / "vep_deepripe_deepsea.parquet"
+        anno_dir / "vep_deepripe_deepsea.parquet",
     shell:
         " ".join(
             [
@@ -147,40 +154,55 @@ rule merge_deepsea_pcas:
             ]
         )
 
+
 rule concat_annotations:
     input:
-        pvcf = metadata_dir / config['pvcf_blocks_file'],
-        anno_dir = anno_dir,
-        vcf_files=
-            expand([anno_dir / f"{source_variant_file_pattern}_merged.parquet"],
+        pvcf=metadata_dir / config["pvcf_blocks_file"],
+        anno_dir=anno_dir,
+        vcf_files=expand(
+            [anno_dir / f"{source_variant_file_pattern}_merged.parquet"],
             zip,
             chr=chromosomes,
-            block=block)
-    output: anno_dir / "vep_deepripe.parquet"
+            block=block,
+        ),
+    output:
+        anno_dir / "vep_deepripe.parquet",
     shell:
-        " ".join([
-            "python",
-            str(annotation_python_file),
-            "concat-annotations",
-            "{input.pvcf}",
-            "{input.anno_dir}",
-            f"{str(source_variant_file_pattern + '_merged.parquet').format(chr='{{chr}}', block='{{block}}')}",
-            "{output}",
-            f" --included-chromosomes {','.join(included_chromosomes)}"
-            ])
+        " ".join(
+            [
+                "python",
+                str(annotation_python_file),
+                "concat-annotations",
+                "{input.pvcf}",
+                "{input.anno_dir}",
+                f"{str(source_variant_file_pattern + '_merged.parquet').format(chr='{{chr}}', block='{{block}}')}",
+                "{output}",
+                f" --included-chromosomes {','.join(included_chromosomes)}",
+            ]
+        )
+
 
 rule merge_annotations:
     input:
-        vep =  anno_dir / (source_variant_file_pattern + "_vep_anno.tsv"),
-        deepripe_parclip =  anno_dir / (source_variant_file_pattern + "_variants.parclip_deepripe.csv.gz"),
-        deepripe_k5 = anno_dir / (source_variant_file_pattern + "_variants.eclip_k5_deepripe.csv.gz"),
-        deepripe_hg2 = anno_dir / (source_variant_file_pattern + "_variants.eclip_hg2_deepripe.csv.gz"),
-        variant_file = variant_file
-
-
+        vep=anno_dir / (source_variant_file_pattern + "_vep_anno.tsv"),
+        deepripe_parclip=anno_dir
+        / (source_variant_file_pattern + "_variants.parclip_deepripe.csv.gz"),
+        deepripe_k5=anno_dir
+        / (source_variant_file_pattern + "_variants.eclip_k5_deepripe.csv.gz"),
+        deepripe_hg2=anno_dir
+        / (source_variant_file_pattern + "_variants.eclip_hg2_deepripe.csv.gz"),
+        variant_file=variant_file,
     output:
         anno_dir / f"{source_variant_file_pattern}_merged.parquet",
-    shell: "HEADER=$(grep  -n  '#Uploaded_variation' "+"{input.vep}" +"| head | cut -f 1 -d ':') && python "+f"{annotation_python_file} "+"merge-annotations $(($HEADER-1)) {input.vep} {input.deepripe_parclip} {input.deepripe_hg2} {input.deepripe_k5} {input.variant_file} {output}"
+    shell:
+        (
+            "HEADER=$(grep  -n  '#Uploaded_variation' "
+            + "{input.vep}"
+            + "| head | cut -f 1 -d ':') && python "
+            + f"{annotation_python_file} "
+            + "merge-annotations $(($HEADER-1)) {input.vep} {input.deepripe_parclip} {input.deepripe_hg2} {input.deepripe_k5} {input.variant_file} {output}"
+        )
+
 
 rule mv_absplice_files:
     input:
@@ -223,7 +245,6 @@ rule absplice:
             block=block,
         ),
         config=absplice_repo_dir / "example" / "workflow" / "mv_config.done",
-
     output:
         expand(
             [
@@ -242,7 +263,10 @@ rule absplice:
         ),
     threads: n_cores_absplice
     shell:
-        f"""python -m snakemake -s {str(absplice_repo_dir/"example"/"workflow"/"Snakefile")} -j 1 --use-conda --rerun-incomplete --directory {str(absplice_repo_dir /"example"/"workflow")} -c"""+"{threads}"
+        (
+            f"""python -m snakemake -s {str(absplice_repo_dir/"example"/"workflow"/"Snakefile")} -j 1 --use-conda --rerun-incomplete --directory {str(absplice_repo_dir /"example"/"workflow")} -c"""
+            + "{threads}"
+        )
 
 
 rule mod_config_absplice:
@@ -251,6 +275,7 @@ rule mod_config_absplice:
     shell:
         f""" rm {absplice_repo_dir}/example/workflow/config.yaml && cp {deeprvat_parent_path}/pipelines/resources/absplice_config.yaml {absplice_repo_dir}/example/workflow/config.yaml && touch {absplice_repo_dir}/example/workflow/mv_config.done"""
 
+
 rule link_files_absplice:
     input:
         anno_tmp_dir / (source_variant_file_pattern + "_variants_header.vcf.gz"),
@@ -262,13 +287,11 @@ rule link_files_absplice:
         f"mkdir -p {absplice_repo_dir/'example/data/resources/analysis_files/input_files'} && ln -s -r {{input}} {{output}}"
 
 
-
 rule deepSea_PCA:
     input:
         anno_dir / "all_variants.wID.deepSea.csv",
     output:
         anno_dir / "deepSea_pca" / "deepsea_pca.parquet",
-
     shell:
         " ".join(
             [
@@ -280,7 +303,7 @@ rule deepSea_PCA:
                 "deepsea-pca",
                 f"--n-components {config['deepsea_pca_n_components']}",
                 "{input}",
-                str(anno_dir / "deepSea_pca"/ "pca_matrix"),
+                str(anno_dir / "deepSea_pca" / "pca_matrix"),
                 str(anno_dir / "deepSea_pca"),
             ]
         )
@@ -291,9 +314,8 @@ rule add_ids_deepSea:
         variant_file=variant_file,
         annotation_file=anno_dir / "all_variants.deepSea.csv",
     output:
-        anno_dir / "all_variants.wID.deepSea.csv"
+        anno_dir / "all_variants.wID.deepSea.csv",
     threads: ncores_addis
-
     shell:
         " ".join(
             [
@@ -312,7 +334,8 @@ rule concat_deepSea:
     input:
         expand(
             [
-                anno_dir / (source_variant_file_pattern + ".CLI.deepseapredict.diff.tsv"),
+                anno_dir
+                / (source_variant_file_pattern + ".CLI.deepseapredict.diff.tsv"),
             ],
             zip,
             chr=chromosomes,
@@ -320,7 +343,6 @@ rule concat_deepSea:
         ),
     output:
         anno_dir / "all_variants.deepSea.csv",
-
     shell:
         " ".join(
         [
@@ -331,9 +353,9 @@ rule concat_deepSea:
             ",".join(included_chromosomes),
             "--sep '\t'",
             f"{anno_dir}",
-            str(source_variant_file_pattern + ".CLI.deepseapredict.diff.tsv").format(
-        chr="{{chr}}", block="{{block}}"
-                ),
+            str(
+        source_variant_file_pattern + ".CLI.deepseapredict.diff.tsv"
+                ).format(chr="{{chr}}", block="{{block}}"),
                 str(metadata_dir / config["pvcf_blocks_file"]),
                 str(
                     anno_dir / "all_variants.deepSea.csv",
@@ -344,7 +366,8 @@ rule concat_deepSea:
 
 rule deepSea:
     input:
-        variants=anno_tmp_dir / (source_variant_file_pattern + "_variants_header.vcf.gz"),
+        variants=anno_tmp_dir
+        / (source_variant_file_pattern + "_variants_header.vcf.gz"),
         fasta=fasta_dir / fasta_file_name,
     output:
         anno_dir / (source_variant_file_pattern + ".CLI.deepseapredict.diff.tsv"),
@@ -354,15 +377,12 @@ rule deepSea:
         "kipoi_veff2_predict {input.variants} {input.fasta} {output} -l 1000 -m 'DeepSEA/predict' -s 'diff'"
 
 
-
-
 rule deepRiPe_parclip:
     input:
         variants=anno_tmp_dir / (source_variant_file_pattern + "_variants.vcf"),
         fasta=fasta_dir / fasta_file_name,
     output:
         anno_dir / (source_variant_file_pattern + "_variants.parclip_deepripe.csv.gz"),
-
     shell:
         f"mkdir -p {pybedtools_tmp_path/'parclip'} && python {annotation_python_file} scorevariants-deepripe {{input.variants}} {anno_dir}  {{input.fasta}} {pybedtools_tmp_path/'parclip'} {saved_deepripe_models_path} {{threads}} 'parclip'"
 
@@ -384,13 +404,11 @@ rule deepRiPe_eclip_k5:
         fasta=fasta_dir / fasta_file_name,
     output:
         anno_dir / (source_variant_file_pattern + "_variants.eclip_k5_deepripe.csv.gz"),
-
     threads: lambda wildcards, attempt: n_jobs_deepripe * attempt
     shell:
         f"mkdir -p {pybedtools_tmp_path/'k5'} && python {annotation_python_file} scorevariants-deepripe {{input.variants}} {anno_dir}  {{input.fasta}} {pybedtools_tmp_path/'k5'} {saved_deepripe_models_path} {{threads}} 'eclip_k5'"
 
 
-
 rule vep:
     input:
         vcf=anno_tmp_dir / (source_variant_file_pattern + "_stripped.vcf.gz"),
@@ -398,7 +416,6 @@ rule vep:
     output:
         anno_dir / (source_variant_file_pattern + "_vep_anno.tsv"),
     threads: vep_nfork
-
     shell:
         " ".join(
             [
@@ -442,13 +459,15 @@ rule vep:
                 f"--plugin CADD,{cadd_snv_file},{cadd_indel_file}",
                 f"--plugin SpliceAI,snv={spliceAI_snv_file},indel={spliceAI_indel_file}",
                 f"--plugin PrimateAI,{primateAIfile}",
-                f"--plugin Condel,{condel_config_path},s,2"
+                f"--plugin Condel,{condel_config_path},s,2",
             ]
         )
 
+
 rule extract_with_header:
     input:
-        source_variant_dir / (source_variant_file_pattern + f".{config['source_variant_file_type']}"),
+        source_variant_dir
+        / (source_variant_file_pattern + f".{config['source_variant_file_type']}"),
     output:
         anno_tmp_dir / (source_variant_file_pattern + "_variants_header.vcf.gz"),
     shell:
@@ -473,7 +492,8 @@ rule strip_chr_name:
 
 rule extract_variants:
     input:
-        source_variant_dir / (source_variant_file_pattern + f".{config['source_variant_file_type']}"),
+        source_variant_dir
+        / (source_variant_file_pattern + f".{config['source_variant_file_type']}"),
     output:
         anno_tmp_dir / (source_variant_file_pattern + "_variants.vcf"),
     shell: