diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk index aaad577..c47edc1 100644 --- a/workflow/rules/common.smk +++ b/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) diff --git a/workflow/rules/stats.smk b/workflow/rules/stats.smk index 776c251..27b2703 100644 --- a/workflow/rules/stats.smk +++ b/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",