From 1a6896926c4f38d897541a6d38dc874d54b57176 Mon Sep 17 00:00:00 2001 From: Alexander Thomas <77535027+alethomas@users.noreply.github.com> Date: Thu, 6 Jan 2022 13:28:28 +0100 Subject: [PATCH] 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 Co-authored-by: Thomas Battenfeld <46334240+thomasbtf@users.noreply.github.com> --- workflow/rules/generate_output.smk | 4 ++-- workflow/rules/strain_calling.smk | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/workflow/rules/generate_output.smk b/workflow/rules/generate_output.smk index 1e9023d69..14b349480 100644 --- 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 index bb836e505..e526a28b2 100644 --- 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",