From 413fe25e524499ea79e78cb1fb9dd95d64671fd5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gordon=20J=2E=20K=C3=B6hn?= <gordon@koehn.net>
Date: Fri, 13 Sep 2024 13:52:44 +0200
Subject: [PATCH] remove some outputs

---
 scripts/amplicon_covs_click.py | 2 ++
 workflows/amplicon_cov.smk     | 3 ++-
 2 files changed, 4 insertions(+), 1 deletion(-)

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 
         """