diff --git a/workflow/rules/generate_output.smk b/workflow/rules/generate_output.smk index 5db0fe226..11899c101 100644 --- a/workflow/rules/generate_output.smk +++ b/workflow/rules/generate_output.smk @@ -37,7 +37,7 @@ rule plot_coverage_main_sequence: expand_samples_for_date("results/{{date}}/qc/samtools_depth/{sample}.txt"), output: report( - "results/{date}/plots/coverage-reference-genome.svg", + "results/{date}/plots/coverage-reference-genome.png", caption="../report/all-main-coverage.rst", category="3. Sequencing Details", subcategory="2. Coverage of Reference Genome", @@ -59,7 +59,7 @@ rule plot_coverage_polished_sequence: ), output: report( - "results/{date}/plots/coverage-assembled-genome.svg", + "results/{date}/plots/coverage-assembled-genome.png", caption="../report/all-final-coverage.rst", category="3. Sequencing Details", subcategory="3. Coverage of Reconstructed Sequences", @@ -379,8 +379,8 @@ rule snakemake_reports_patient: ), # 3. Sequencing Details "results/{date}/qc/laboratory/multiqc.html", - "results/{date}/plots/coverage-reference-genome.svg", - "results/{date}/plots/coverage-assembled-genome.svg", + "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 [], @@ -439,7 +439,7 @@ use rule snakemake_reports_patient as snakemake_reports_environment with: ), # 3. Sequencing Details "results/{date}/qc/laboratory/multiqc.html", - "results/{date}/plots/coverage-reference-genome.svg", + "results/{date}/plots/coverage-reference-genome.png", output: "results/environment-reports/{date}.zip", log: