Tried fixing formatting

workflow/rules/common.smk

@@ -156,8 +156,16 @@ def is_ion_torrent(wildcards, sample=None):
 def has_pseudo_assembly(wildcards, sample=None):
     """Returns if a pseudo-assembly should be created for the sample."""
     if sample is None:
-        return is_illumina(wildcards) or is_ion_torrent(wildcards) or is_illumina_se(wildacrds)
-    return is_illumina(None, sample) or is_ion_torrent(None, sample) or is_illumina_se(None, sample)
+        return (
+            is_illumina(wildcards)
+            or is_ion_torrent(wildcards)
+            or is_illumina_se(wildacrds)
+        )
+    return (
+        is_illumina(None, sample)
+        or is_ion_torrent(None, sample)
+        or is_illumina_se(None, sample)
+    )
 
 
 def has_consensus_assembly(wildcards, sample=None):
@@ -170,8 +178,14 @@ def has_consensus_assembly(wildcards, sample=None):
 def is_single_end(wildcards, sample=None):
     """Returns if the sample was sequenced with single end technology."""
     if sample is None:
-        return is_ont(wildcards) or is_ion_torrent(wildcards) or is_illumina_se(wildacrds)
-    return is_ont(None, sample) or is_ion_torrent(None, sample) or is_illumina_se(None, sample)
+        return (
+            is_ont(wildcards) or is_ion_torrent(wildcards) or is_illumina_se(wildacrds)
+        )
+    return (
+        is_ont(None, sample)
+        or is_ion_torrent(None, sample)
+        or is_illumina_se(None, sample)
+    )
 
 
 def get_fastqs(wildcards):
@@ -363,9 +377,11 @@ def get_non_cov2_calls(from_caller="pangolin"):
     pattern = (
         "results/benchmarking/tables/strain-calls/non-cov2-{accession}.polished.strains.pangolin.csv"
         if from_caller == "pangolin"
-        else "results/benchmarking/tables/strain-calls/non-cov2-{accession}.strains.kallisto.tsv"
-        if from_caller == "kallisto"
-        else []
+        else (
+            "results/benchmarking/tables/strain-calls/non-cov2-{accession}.strains.kallisto.tsv"
+            if from_caller == "kallisto"
+            else []
+        )
     )
 
     if not pattern:
@@ -421,7 +437,7 @@ def get_reads(wildcards):
             "results/{date}/trimmed/fastp-pe/{sample}.{read}.fastq.gz",
             read=[1, 2],
             **wildcards,
-        )  
+        )
 
         illumina_se_pattern = expand(
             "results/{date}/trimmed/fastp-se/{sample}.fastq.gz",
@@ -862,9 +878,7 @@ def get_varlociraptor_bias_flags(wildcards):
         )
     if is_amplicon_data(wildcards.sample):
         # no bias detection possible
-        return (
-            "--omit-strand-bias --omit-read-orientation-bias --omit-read-position-bias --omit-softclip-bias"
-        )
+        return "--omit-strand-bias --omit-read-orientation-bias --omit-read-position-bias --omit-softclip-bias"
     return ""
 
 
@@ -1145,18 +1159,22 @@ def get_fallbacks_for_report(fallback_type):
         if fallback_type == "pseudo":
             path = "results/{{date}}/contigs/pseudoassembled/{sample}.fasta"
             return [
-                path.format(sample=sample)
-                if has_pseudo_assembly(None, sample)
-                else "resources/genomes/main.fasta"
+                (
+                    path.format(sample=sample)
+                    if has_pseudo_assembly(None, sample)
+                    else "resources/genomes/main.fasta"
+                )
                 for sample in get_samples_for_date(wildcards.date)
             ]
 
         elif fallback_type == "consensus":
             path = "results/{{date}}/contigs/masked/consensus/{sample}.fasta"
             return [
-                path.format(sample=sample)
-                if has_consensus_assembly(None, sample)
-                else "resources/genomes/main.fasta"
+                (
+                    path.format(sample=sample)
+                    if has_consensus_assembly(None, sample)
+                    else "resources/genomes/main.fasta"
+                )
                 for sample in samples
             ]
 
@@ -1446,9 +1464,11 @@ def get_kallisto_quant_extra(wildcards, input):
         return get_if_testing("--single --fragment-length 250 --sd 47301")
 
     return (
-        f"--single --fragment-length {get_first_line(input.fragment_length)} --sd {get_first_line(input.standard_deviation)}"
-        if is_single_end(wildcards)
-        else "",
+        (
+            f"--single --fragment-length {get_first_line(input.fragment_length)} --sd {get_first_line(input.standard_deviation)}"
+            if is_single_end(wildcards)
+            else ""
+        ),
     )
 
 
@@ -1747,4 +1767,3 @@ wildcard_constraints:
         list(map(re.escape, config["variant-calling"]["filters"])) + ["nofilter"]
     ),
     varrange="structural|small|homopolymer-medaka|homopolymer-longshot|lineage-variants",
-

workflow/rules/generate_output.smk

@@ -381,9 +381,11 @@ rule snakemake_reports_patient:
         "results/{date}/qc/laboratory/multiqc.html",
         "results/{date}/plots/coverage-reference-genome.png",
         "results/{date}/plots/coverage-assembled-genome.png",
-        lambda wildcards: "results/{date}/plots/primer-clipping-intervals.svg"
-        if any_sample_is_amplicon(wildcards)
-        else [],
+        lambda wildcards: (
+            "results/{date}/plots/primer-clipping-intervals.svg"
+            if any_sample_is_amplicon(wildcards)
+            else []
+        ),
         # 4. Assembly
         "results/{date}/filter-overview",
         "results/{date}/pangolin-call-overview",

workflow/rules/ref.smk

@@ -20,9 +20,11 @@ rule get_genome:
         "resources/genomes/{accession}.fasta",
     params:
         accession=(
-            lambda w: config["virus-reference-genome"]
-            if w.accession == "main"
-            else w.accession
+            lambda w: (
+                config["virus-reference-genome"]
+                if w.accession == "main"
+                else w.accession
+            )
         ),
     log:
         "logs/genomes/get-genome/{accession}.log",

workflow/rules/variant_calling.smk

@@ -75,9 +75,11 @@ rule longshot:
             "results/{date}/candidate-calls/ref~{reference}/{sample}.homopolymer-longshot.vcf"
         ),
     params:
-        reference_name=lambda w: config["virus-reference-genome"]
-        if w.reference == "main"
-        else f"{w.reference}.1",
+        reference_name=lambda w: (
+            config["virus-reference-genome"]
+            if w.reference == "main"
+            else f"{w.reference}.1"
+        ),
     log:
         "logs/{date}/longshot/ref~{reference}/{sample}.log",
     conda: