fix: wrong enumeration with kallisto included (#439)

* fix: wromg enumeration with kallisto included * refactor: change order of category 1 subcategores * Update generate_output.smk * Update generate_output.smk Co-authored-by: Thomas Battenfeld <[email protected]> Co-authored-by: Thomas Battenfeld <[email protected]>
IKIM-Essen · Jan 6, 2022 · 1a68969 · 1a68969
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commit 1a68969
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diff --git a/workflow/rules/generate_output.smk b/workflow/rules/generate_output.smk
@@ -258,7 +258,7 @@ rule plot_lineages_over_time:
             "results/{date}/plots/lineages-over-time.svg",
             caption="../report/lineages-over-time.rst",
             category="1. Overview",
-            subcategory="2. Lineages Development",
+            subcategory="2. Lineage Development",
         ),
         "results/{date}/tables/lineages-over-time.csv",
     params:
@@ -290,7 +290,7 @@ rule plot_variants_over_time:
             "results/{date}/plots/variants-{ORFNAME}-over-time.svg",
             caption="../report/variants-over-time.rst",
             category="1. Overview",
-            subcategory="3. Variants Development",
+            subcategory="5. Variant Development",
         ),
         "results/{date}/tables/variants-{ORFNAME}-over-time.csv",
     params:

diff --git a/workflow/rules/strain_calling.smk b/workflow/rules/strain_calling.smk
@@ -128,7 +128,7 @@ rule kallisto_plot_all_strains:
             "results/{date}/plots/all.{mode,(major|any)}-strain.strains.kallisto.svg",
             caption="../report/all-strain-calls-kallisto.rst",
             category="1. Overview",
-            subcategory="2. Strain Calls",
+            subcategory="3. Lineage Calls",
         ),
     log:
         "logs/{date}/plot-strains/all.{mode}.log",
@@ -169,7 +169,7 @@ rule pangolin_plot_all_strains:
             "results/{date}/plots/all.strains.pangolin.svg",
             caption="../report/all-strain-calls-pangolin.rst",
             category="1. Overview",
-            subcategory="2. Strain Calls",
+            subcategory="3. Lineage Calls",
         ),
     log:
         "logs/{date}/plot-strains-pangolin/all.log",