fmt

Author: johanneskoester

workflow/rules/common.smk

@@ -70,7 +70,9 @@ def get_trimmed_reads(wildcards):
     if not is_single_end(**wildcards):
         # paired-end sample
         return expand(
-            "results/trimmed/{sample}-{unit}.{group}.fastq.gz", group=[1, 2], **wildcards
+            "results/trimmed/{sample}-{unit}.{group}.fastq.gz",
+            group=[1, 2],
+            **wildcards
         )
     # single end sample
     return "results/trimmed/{sample}-{unit}.fastq.gz".format(**wildcards)

workflow/rules/stats.smk

@@ -2,7 +2,11 @@ rule vcf_to_tsv:
     input:
         "results/annotated/all.vcf.gz",
     output:
-        report("results/tables/calls.tsv.gz", caption="../report/calls.rst", category="Calls"),
+        report(
+            "results/tables/calls.tsv.gz",
+            caption="../report/calls.rst",
+            category="Calls",
+        ),
     log:
         "logs/vcf-to-tsv.log",
     conda:
@@ -21,7 +25,9 @@ rule plot_stats:
             "results/plots/depths.svg", caption="../report/depths.rst", category="Plots"
         ),
         freqs=report(
-            "results/plots/allele-freqs.svg", caption="../report/freqs.rst", category="Plots"
+            "results/plots/allele-freqs.svg",
+            caption="../report/freqs.rst",
+            category="Plots",
         ),
     log:
         "logs/plot-stats.log",