From f6fd4974a747e2a8dfe68704499298682a4890df Mon Sep 17 00:00:00 2001
From: thomasmanke <manke@ie-freiburg.mpg.de>
Date: Wed, 7 Aug 2024 16:13:09 +0200
Subject: [PATCH] fix doc styling

---
 docs/conf.py                         | 12 +++++++-----
 docs/content/workflows/makePairs.rst | 22 +++++++++++-----------
 2 files changed, 18 insertions(+), 16 deletions(-)

diff --git a/docs/conf.py b/docs/conf.py
index e99166a43..773f0ce91 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -143,12 +143,14 @@
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-on_rtd = os.environ.get('READTHEDOCS', None) == 'True'
+# on_rtd = os.environ.get('READTHEDOCS', None) == 'True'
 
-if not on_rtd:  # only import and set the theme if we're building docs locally
-    import sphinx_rtd_theme
-    html_theme = 'sphinx_rtd_theme'  # 'alabaster' 'sphinx_rtd_theme'
-    html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
+#if not on_rtd:  # only import and set the theme if we're building docs locally
+
+# import them both locally and on rtd
+import sphinx_rtd_theme
+html_theme = 'sphinx_rtd_theme'  # 'alabaster' 'sphinx_rtd_theme'
+html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
diff --git a/docs/content/workflows/makePairs.rst b/docs/content/workflows/makePairs.rst
index dc5a0b040..b1e6ccba4 100644
--- a/docs/content/workflows/makePairs.rst
+++ b/docs/content/workflows/makePairs.rst
@@ -96,18 +96,18 @@ Structure of output directory
 -----------------------------
 
 In addition to the FASTQ module results (see :ref:`running_snakePipes`), the workflow produces the following outputs::
-    
+
     .
-    ├── bam
-    ├── FASTQ
-    ├── FastQC
-    ├── FastQC_trimmed
-    ├── FASTQ_fastp
-    ├── genome
-    ├── multiqc
-    ├── originalFASTQ
-    ├── pairs
-    └── phase_stats
+    |-- bam
+    |-- FASTQ
+    |-- FastQC
+    |-- FastQC_trimmed
+    |-- FASTQ_fastp
+    |-- genome
+    |-- multiqc
+    |-- originalFASTQ
+    |-- pairs
+    |-- phase_stats
  
 
 * **bam** folder contains the mapping results in BAM format. The files were obtained after running `bwa <https://github.com/lh3/bwa>`__ in paired-end mode.