diff --git a/scripts/amplicon_covs_click.py b/scripts/amplicon_covs_click.py index b51deff..0602fca 100644 --- a/scripts/amplicon_covs_click.py +++ b/scripts/amplicon_covs_click.py @@ -329,6 +329,8 @@ def main( click.echo("Outputting plots.") make_cov_heatmap(all_covs, os.path.join(outdir, "cov_heatmap.pdf")) + print("Making median cov hist") + make_median_cov_hist(all_covs, os.path.join(outdir, "median_cov_hist.pdf")) make_median_coverage_barplot( all_covs, os.path.join(outdir, "median_coverage_barplot.pdf") diff --git a/workflows/amplicon_cov.smk b/workflows/amplicon_cov.smk index daba1a2..702de9c 100644 --- a/workflows/amplicon_cov.smk +++ b/workflows/amplicon_cov.smk @@ -59,7 +59,8 @@ rule relative_amplicon_coverage_per_batch: -f {input.samples} \ -r {params.primers_fp} \ -o {params.output_dir} \ - -p + -p \ + -v """