diff --git a/.ruff.toml b/.ruff.toml
deleted file mode 100644
index f11cf63..0000000
--- a/.ruff.toml
+++ /dev/null
@@ -1 +0,0 @@
-line-length = 120
diff --git a/Snakefile b/Snakefile
index e15b6a7..6f0dab6 100644
--- a/Snakefile
+++ b/Snakefile
@@ -1,7 +1,6 @@
 import csv
 import os
 import pandas as pd
-import warnings
 from pathlib import Path
 
 from utils import get, perform
@@ -551,10 +550,10 @@ def fastqc_dump_fastq_input(wildcards):
     if perform.prefetch(config):
         if str(wildcards.PE_SE) == "1":
             return [
-                checkpoints.fasterq_dump.get(tissue_name=wildcards.tissue_name, tag=wildcards.tag, PE_SE="1").output[0],
-                checkpoints.fasterq_dump.get(tissue_name=wildcards.tissue_name, tag=wildcards.tag, PE_SE="2").output[0],
+                checkpoints.fasterq_dump.get(tissue_name=wildcards.tissue_name, tag=wildcards.tag, PE_SE="1").output[0],  # type: ignore
+                checkpoints.fasterq_dump.get(tissue_name=wildcards.tissue_name, tag=wildcards.tag, PE_SE="2").output[0],  # type: ignore
             ]
-        return checkpoints.fasterq_dump.get(tissue_name=wildcards.tissue_name, tag=wildcards.tag, PE_SE="S").output
+        return checkpoints.fasterq_dump.get(tissue_name=wildcards.tissue_name, tag=wildcards.tag, PE_SE="S").output  # type: ignore
 
     # Make sure we are able to load local FastQ files
     if "LOCAL_FASTQ_FILES" in config.keys() and os.path.exists(config["LOCAL_FASTQ_FILES"]):
@@ -649,7 +648,7 @@ def contaminant_screen_input(wildcards):
 
     # If we have performed fasterq_dump, return its output
     if perform.dump_fastq(config):
-        return checkpoints.fasterq_dump.get(**wildcards).output
+        return checkpoints.fasterq_dump.get(**wildcards).output  # type: ignore
 
     # Otherwise collect local files
     fastq_files = Path(config["LOCAL_FASTQ_FILES"])
@@ -691,10 +690,10 @@ def get_trim_input(wildcards):
     if perform.dump_fastq(config):
         if str(wildcards.PE_SE) in ["1", "2"]:
             return [
-                *checkpoints.fasterq_dump.get(tissue_name=wildcards.tissue_name, tag=wildcards.tag, PE_SE="1").output,
-                *checkpoints.fasterq_dump.get(tissue_name=wildcards.tissue_name, tag=wildcards.tag, PE_SE="2").output,
+                *checkpoints.fasterq_dump.get(tissue_name=wildcards.tissue_name, tag=wildcards.tag, PE_SE="1").output,  # type: ignore
+                *checkpoints.fasterq_dump.get(tissue_name=wildcards.tissue_name, tag=wildcards.tag, PE_SE="2").output,  # type: ignore
             ]
-        return checkpoints.fasterq_dump.get(tissue_name=wildcards.tissue_name, tag=wildcards.tag, PE_SE="S").output
+        return checkpoints.fasterq_dump.get(tissue_name=wildcards.tissue_name, tag=wildcards.tag, PE_SE="S").output  # type: ignore
     else:
         files = list(
             Path(config["LOCAL_FASTQ_FILES"]).rglob("{tissue_name}_{tag}_{PE_SE}.fastq.gz".format(**wildcards))
@@ -750,11 +749,11 @@ checkpoint trim:
 
 def get_fastqc_trim_input(wildcards):
     if wildcards.PE_SE == "1":
-        forward = str(checkpoints.trim.get(tissue_name=wildcards.tissue_name, tag=wildcards.tag, PE_SE="1").output)
-        reverse = str(checkpoints.trim.get(tissue_name=wildcards.tissue_name, tag=wildcards.tag, PE_SE="2").output)
+        forward = str(checkpoints.trim.get(tissue_name=wildcards.tissue_name, tag=wildcards.tag, PE_SE="1").output)  # type: ignore
+        reverse = str(checkpoints.trim.get(tissue_name=wildcards.tissue_name, tag=wildcards.tag, PE_SE="2").output)  # type: ignore
         return [forward, reverse]
     else:
-        return checkpoints.trim.get(tissue_name=wildcards.tissue_name, tag=wildcards.tag, PE_SE="S").output
+        return checkpoints.trim.get(tissue_name=wildcards.tissue_name, tag=wildcards.tag, PE_SE="S").output  # type: ignore
 
 
 rule fastqc_trim:
@@ -811,20 +810,20 @@ def star_input(wildcards):
     if perform.trim(config):
         items.extend(
             [
-                *checkpoints.trim.get(tissue_name=wildcards.tissue_name, tag=wildcards.tag, PE_SE="1").output,
-                *checkpoints.trim.get(tissue_name=wildcards.tissue_name, tag=wildcards.tag, PE_SE="2").output,
+                *checkpoints.trim.get(tissue_name=wildcards.tissue_name, tag=wildcards.tag, PE_SE="1").output,  # type: ignore
+                *checkpoints.trim.get(tissue_name=wildcards.tissue_name, tag=wildcards.tag, PE_SE="2").output,  # type: ignore
             ]
             if is_paired_end
-            else [*checkpoints.trim.get(tissue_name=wildcards.tissue_name, tag=wildcards.tag, PE_SE="S").output]
+            else [*checkpoints.trim.get(tissue_name=wildcards.tissue_name, tag=wildcards.tag, PE_SE="S").output]  # type: ignore
         )
     elif perform.dump_fastq(config):
         items.extend(
             [
-                *checkpoints.fasterq_dump.get(tissue_name=wildcards.tissue_name, tag=wildcards.tag, PE_SE="1").output,
-                *checkpoints.fasterq_dump.get(tissue_name=wildcards.tissue_name, tag=wildcards.tag, PE_SE="2").output,
+                *checkpoints.fasterq_dump.get(tissue_name=wildcards.tissue_name, tag=wildcards.tag, PE_SE="1").output,  # type: ignore
+                *checkpoints.fasterq_dump.get(tissue_name=wildcards.tissue_name, tag=wildcards.tag, PE_SE="2").output,  # type: ignore
             ]
             if is_paired_end
-            else [*checkpoints.fasterq_dump.get(tissue_name=wildcards.tissue_name, tag=wildcards.tag, PE_SE="S").output]
+            else [*checkpoints.fasterq_dump.get(tissue_name=wildcards.tissue_name, tag=wildcards.tag, PE_SE="S").output]  # type: ignore
         )
     else:
         for file in Path(config["LOCAL_FASTQ_FILES"]).rglob(f"*{file_pattern}"):
diff --git a/cluster/config.yaml b/cluster/config.yaml
deleted file mode 100644
index 615ecbc..0000000
--- a/cluster/config.yaml
+++ /dev/null
@@ -1,41 +0,0 @@
-# This file configures various settings for snakemake to execute jobs to a SLURM cluster.
-# FROM: https://github.com/jdblischak/smk-simple-slurm
-
-cluster:
-  mkdir -p logs/{rule}/{resources.tissue_name} &&
-  sbatch
-    --job-name=smk-{rule}-{wildcards}
-    --account=helikarlab
-    --cpus-per-task={threads}
-    --output=logs/{rule}/{resources.tissue_name}/{rule}-{wildcards}.out
-    --mem={resources.mem_mb}
-    --time={resources.runtime}
-    --parsable
-
-default-resources:
-  - mem_mb=2048
-
-# Job submittion
-cores: 16  # max cores used in snakefile
-cluster-cancel: scancel
-cluster-cancel-nargs: 50
-restart-times: 0
-max-jobs-per-second: 10
-max-status-checks-per-second: 5
-latency-wait: 60
-jobs: 250
-
-# Other settings
-printshellcmds: True
-rerun-incomplete: True
-
-groups:
-  - preroundup=preroundup_group
-  - copy_gene_counts=copy_group
-  - copy_rnaseq_metrics=copy_group
-  - copy_insert_size=copy_group
-  - copy_fragment_size=copy_group
-
-# Do not change these settings. This pipeline will fail to execute if they are changed
-use-conda: True
-conda-frontend: mamba