diff --git a/workflow/Snakefile b/workflow/Snakefile
index 06570ec..26055ed 100644
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -64,9 +64,7 @@ rule finish:
             sample=pd.unique(samples_table.index.values),
         ),
         intersect_sam=expand(
-            OUT_DIR
-            / "{sample}"
-            / "alignments_intersecting_mirna_sorted_tag.sam",
+            OUT_DIR / "{sample}" / "alignments_intersecting_mirna_sorted_tag.sam",
             sample=pd.unique(samples_table.index.values),
         ),
         table=expand(
diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
index 4bf25bc..1565371 100644
--- a/workflow/rules/common.smk
+++ b/workflow/rules/common.smk
@@ -6,9 +6,7 @@
 def get_sample(column_id: str, sample_id: int = None) -> str:
     """Get relevant per sample information."""
     if sample_id:
-        return str(
-            samples_table[column_id][samples_table.index == sample_id].iloc[0]
-        )
+        return str(samples_table[column_id][samples_table.index == sample_id].iloc[0])
     else:
         return str(samples_table[column_id].iloc[0])
 
diff --git a/workflow/rules/map.smk b/workflow/rules/map.smk
index 672b9c5..effa9a6 100644
--- a/workflow/rules/map.smk
+++ b/workflow/rules/map.smk
@@ -83,16 +83,13 @@ rule finish_map:
 rule start:
     input:
         reads=lambda wildcards: expand(
-            pd.Series(
-                samples_table.loc[wildcards.sample, "sample_file"]
-            ).values,
+            pd.Series(samples_table.loc[wildcards.sample, "sample_file"]).values,
             format=convert_lib_format(get_sample("format")),
         ),
     output:
         reads=OUT_DIR / "{sample}" / "{format}" / "reads.{format}",
     params:
-        cluster_log=CLUSTER_LOG
-        / "uncompress_zipped_files_{sample}_{format}.log",
+        cluster_log=CLUSTER_LOG / "uncompress_zipped_files_{sample}_{format}.log",
     log:
         LOCAL_LOG / "uncompress_zipped_files_{sample}_{format}.log",
     container:
@@ -189,9 +186,7 @@ rule remove_adapters:
     output:
         reads=OUT_DIR / "{sample}" / "reads_trimmed_adapters.fasta",
     params:
-        adapter=lambda wildcards: get_sample(
-            "adapter", wildcards.sample
-        ).upper(),
+        adapter=lambda wildcards: get_sample("adapter", wildcards.sample).upper(),
         error_rate=config["error_rate"],
         minimum_length=config["minimum_length"],
         overlap=config["overlap"],
@@ -283,8 +278,7 @@ rule map_transcriptome_segemehl:
     input:
         reads=OUT_DIR / "{sample}" / "reads_collapsed.fasta",
         transcriptome=OUT_DIR / "transcriptome_trimmed_id.fa",
-        transcriptome_index_segemehl=OUT_DIR
-        / "segemehl_transcriptome_index.idx",
+        transcriptome_index_segemehl=OUT_DIR / "segemehl_transcriptome_index.idx",
     output:
         tmap=OUT_DIR / "{sample}" / "segemehl_transcriptome_mappings.sam",
     params:
@@ -650,8 +644,7 @@ rule remove_header_transcriptome_mappings:
     output:
         tmap=OUT_DIR / "{sample}" / "transcriptome_mappings_no_header.sam",
     params:
-        cluster_log=CLUSTER_LOG
-        / "remove_header_transcriptome_mappings_{sample}.log",
+        cluster_log=CLUSTER_LOG / "remove_header_transcriptome_mappings_{sample}.log",
     log:
         LOCAL_LOG / "remove_header_transcriptome_mappings_{sample}.log",
     container:
@@ -762,8 +755,7 @@ rule sort_maps_by_id:
 rule remove_inferiors:
     input:
         sort=OUT_DIR / "{sample}" / "mappings_all_sorted_by_id.sam",
-        script=SCRIPTS_DIR
-        / "sam_remove_duplicates_inferior_alignments_multimappers.pl",
+        script=SCRIPTS_DIR / "sam_remove_duplicates_inferior_alignments_multimappers.pl",
     output:
         remove_inf=OUT_DIR / "{sample}" / "mappings_all_removed_inferiors.sam",
     params:
diff --git a/workflow/rules/quantify.smk b/workflow/rules/quantify.smk
index 422635a..15aa1e7 100644
--- a/workflow/rules/quantify.smk
+++ b/workflow/rules/quantify.smk
@@ -61,12 +61,8 @@ localrules:
 
 rule finish_quantify:
     input:
-        primir_intersect_sam=OUT_DIR
-        / "{sample}"
-        / "alignments_intersecting_primir.sam",
-        mirna_intersect_sam=OUT_DIR
-        / "{sample}"
-        / "alignments_intersecting_mirna.sam",
+        primir_intersect_sam=OUT_DIR / "{sample}" / "alignments_intersecting_primir.sam",
+        mirna_intersect_sam=OUT_DIR / "{sample}" / "alignments_intersecting_mirna.sam",
         intersect_sam=OUT_DIR
         / "{sample}"
         / "alignments_intersecting_mirna_sorted_tag.sam",
@@ -131,8 +127,7 @@ rule filter_sam_by_intersecting_primir:
     output:
         sam=OUT_DIR / "{sample}" / "alignments_intersecting_primir.sam",
     params:
-        cluster_log=CLUSTER_LOG
-        / "filter_sam_by_intersecting_primir_{sample}.log",
+        cluster_log=CLUSTER_LOG / "filter_sam_by_intersecting_primir_{sample}.log",
     log:
         LOCAL_LOG / "filter_sam_by_intersecting_primir_{sample}.log",
     container:
@@ -159,8 +154,7 @@ rule convert_intersecting_primir_sam_to_bam:
     output:
         maps=OUT_DIR / "{sample}" / "alignments_intersecting_primir.bam",
     params:
-        cluster_log=CLUSTER_LOG
-        / "convert_intersecting_primir_sam_to_bam_{sample}.log",
+        cluster_log=CLUSTER_LOG / "convert_intersecting_primir_sam_to_bam_{sample}.log",
     log:
         LOCAL_LOG / "convert_intersecting_primir_sam_to_bam_{sample}.log",
     container:
@@ -203,9 +197,7 @@ rule index_intersecting_primir_bam:
     input:
         maps=OUT_DIR / "{sample}" / "alignments_intersecting_primir_sorted.bam",
     output:
-        maps=OUT_DIR
-        / "{sample}"
-        / "alignments_intersecting_primir_sorted.bam.bai",
+        maps=OUT_DIR / "{sample}" / "alignments_intersecting_primir_sorted.bam.bai",
     params:
         cluster_log=CLUSTER_LOG / "index_intersecting_primir_bam_{sample}.log",
     log:
@@ -225,9 +217,7 @@ rule index_intersecting_primir_bam:
 
 rule intersect_extended_mirna:
     input:
-        alignment=OUT_DIR
-        / "{sample}"
-        / "alignments_intersecting_primir_sorted.bam",
+        alignment=OUT_DIR / "{sample}" / "alignments_intersecting_primir_sorted.bam",
         mirna=expand(
             OUT_DIR / "extended_mirna_annotation_{extension}_nt.gff3",
             extension=config["extension"],
@@ -266,8 +256,7 @@ rule filter_sam_by_intersecting_mirna:
     output:
         sam=OUT_DIR / "{sample}" / "alignments_intersecting_mirna.sam",
     params:
-        cluster_log=CLUSTER_LOG
-        / "filter_sam_by__intersecting_mirna_{sample}.log",
+        cluster_log=CLUSTER_LOG / "filter_sam_by__intersecting_mirna_{sample}.log",
     log:
         LOCAL_LOG / "filter_sam_by_intersecting_mirna_{sample}.log",
     container:
@@ -322,12 +311,9 @@ rule sort_intersecting_mirna_by_feat_tag:
     input:
         sam=OUT_DIR / "{sample}" / "alignments_intersecting_mirna_tag.sam",
     output:
-        sam=OUT_DIR
-        / "{sample}"
-        / "alignments_intersecting_mirna_sorted_tag.sam",
+        sam=OUT_DIR / "{sample}" / "alignments_intersecting_mirna_sorted_tag.sam",
     params:
-        cluster_log=CLUSTER_LOG
-        / "sort_intersecting_mirna_by_feat_tag_{sample}.log",
+        cluster_log=CLUSTER_LOG / "sort_intersecting_mirna_by_feat_tag_{sample}.log",
     log:
         LOCAL_LOG / "sort_intersecting_mirna_by_feat_tag_{sample}.log",
     container:
@@ -345,9 +331,7 @@ rule sort_intersecting_mirna_by_feat_tag:
 
 rule quantify_mirna:
     input:
-        alignments=OUT_DIR
-        / "{sample}"
-        / "alignments_intersecting_mirna_sorted_tag.sam",
+        alignments=OUT_DIR / "{sample}" / "alignments_intersecting_mirna_sorted_tag.sam",
         script=SCRIPTS_DIR / "mirna_quantification.py",
     output:
         table=OUT_DIR / "TABLES" / "mirna_counts_{sample}",
@@ -448,9 +432,7 @@ rule uncollapse_reads:
         maps=OUT_DIR / "{sample}" / "alignments_intersecting_mirna.sam",
         script=SCRIPTS_DIR / "sam_uncollapse.pl",
     output:
-        maps=OUT_DIR
-        / "{sample}"
-        / "alignments_intersecting_mirna_uncollapsed.sam",
+        maps=OUT_DIR / "{sample}" / "alignments_intersecting_mirna_uncollapsed.sam",
     params:
         cluster_log=CLUSTER_LOG / "uncollapse_reads_{sample}.log",
     log:
@@ -474,16 +456,11 @@ rule uncollapse_reads:
 
 rule convert_uncollpased_reads_sam_to_bam:
     input:
-        maps=OUT_DIR
-        / "{sample}"
-        / "alignments_intersecting_mirna_uncollapsed.sam",
+        maps=OUT_DIR / "{sample}" / "alignments_intersecting_mirna_uncollapsed.sam",
     output:
-        maps=OUT_DIR
-        / "{sample}"
-        / "alignments_intersecting_mirna_uncollapsed.bam",
+        maps=OUT_DIR / "{sample}" / "alignments_intersecting_mirna_uncollapsed.bam",
     params:
-        cluster_log=CLUSTER_LOG
-        / "convert_uncollapsed_reads_sam_to_bam_{sample}.log",
+        cluster_log=CLUSTER_LOG / "convert_uncollapsed_reads_sam_to_bam_{sample}.log",
     log:
         LOCAL_LOG / "convert_uncollapsed_reads_sam_to_bam_{sample}.log",
     container:
@@ -501,16 +478,13 @@ rule convert_uncollpased_reads_sam_to_bam:
 
 rule sort_uncollpased_reads_bam_by_position:
     input:
-        maps=OUT_DIR
-        / "{sample}"
-        / "alignments_intersecting_mirna_uncollapsed.bam",
+        maps=OUT_DIR / "{sample}" / "alignments_intersecting_mirna_uncollapsed.bam",
     output:
         maps=OUT_DIR
         / "{sample}"
         / "alignments_intersecting_mirna_uncollapsed_sorted.bam",
     params:
-        cluster_log=CLUSTER_LOG
-        / "sort_uncollapsed_reads_bam_by_position_{sample}.log",
+        cluster_log=CLUSTER_LOG / "sort_uncollapsed_reads_bam_by_position_{sample}.log",
     log:
         LOCAL_LOG / "sort_uncollapsed_reads_bam_by_position_{sample}.log",
     container: