escape wildcard characters

ktmeaton · Aug 14, 2020 · ab8aaba · ab8aaba
1 parent 027d098
commit ab8aaba
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Showing 2 changed files with 10 additions and 8 deletions.
diff --git a/main.nf b/main.nf
@@ -199,7 +199,7 @@ if (!params.skip_ncbimeta_db_create && params.ncbimeta_create){
      Publish:
      ncbimeta_sqlite_db (sqlite): NCBImeta SQLite database.
      ncbimeta_yaml (yaml): NCBImeta config file.
-     *.log (text): Text logs of NCBImeta database creation.
+     \*.log (text): Text logs of NCBImeta database creation.
 
     */
 
@@ -240,8 +240,8 @@ if(!params.skip_ncbimeta_db_update && params.ncbimeta_update){
 
     Publish:
     ncbimeta_yaml (yaml): NCBImeta config file.
-    *.log (text): Text logs of NCBImeta database update.
-    *.txt (text): Text export of NCBImeta database.
+    \*.log (text): Text logs of NCBImeta database update.
+    \*.txt (text): Text export of NCBImeta database.
 
     */
 
@@ -1289,8 +1289,8 @@ process snippy_multi_filter{
 
   Publish:
   snippy_core_full_aln.filter\*.fasta (fasta): Multi fasta of filtered chromosome genome sites.
-  *.fasta (fasta): All loci extracted fasta files.
-  *.bed (bed): All loci bed coordinate files for extraction.
+  \*.fasta (fasta): All loci extracted fasta files.
+  \*.bed (bed): All loci bed coordinate files for extraction.
 
   */
   // Other variables and config
@@ -1772,7 +1772,7 @@ process multiqc{
 
   Publish:
   multiqc_report.html (html): MultiQC report file.
-  *_data (misc): All default MultiQC data files.
+  \*_data (misc): All default MultiQC data files.
 
   */
   // Other variables and config

diff --git a/scripts/process_docs.py b/scripts/process_docs.py
@@ -66,7 +66,7 @@
 H2_CHAR = "*"
 H3_CHAR = "-"
 TABLE_CHAR = "="
-TABLE_COL_WIDTH = 40
+TABLE_COL_WIDTH = 50
 # -----------------------------------------------------------------------------#
 #                               Processing                                     #
 # -----------------------------------------------------------------------------#
@@ -77,7 +77,9 @@
         if line.startswith("// Section: "):
             split_section = line.split("Section: ")
             section_name = split_section[1]
-            rst_file.write(section_name + "\n" + H2_CHAR * len(section_name) + "\n")
+            rst_file.write(
+                "\n" + section_name + "\n" + H2_CHAR * len(section_name) + "\n"
+            )
         # Skip everything else that is not process
         if line.startswith("process"):
             # Parse the process lines