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fix: reduce loading time of coverage plots #498

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merged 2 commits into from
Mar 21, 2022
Merged

fix: reduce loading time of coverage plots #498

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8c7f480
change from svg to png
thomasbtf Mar 14, 2022
2f7eaef
Merge branch 'master' into fix-cov-plot-loading
thomasbtf Mar 16, 2022
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10 changes: 5 additions & 5 deletions workflow/rules/generate_output.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand All @@ -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",
Expand Down Expand Up @@ -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 [],
Expand Down Expand Up @@ -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:
Expand Down