Merge branch 'pairtools' of github.com:maxplanck-ie/snakepipes into p…

…airtools

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

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.