Moved the shell script to course contents

Author: apalleja

scripts/align_and_count_shell_script.md …contents/align_and_count_shell_script.mdscripts/align_and_count_shell_script.md renamed to course_contents/align_and_count_shell_script.md scripts/align_and_count_shell_script.md renamed to course_contents/align_and_count_shell_script.md

@@ -31,6 +31,7 @@ course_information/Timing.md
 course_contents/DockerIntro.md
 course_contents/HandsOn.md
 course_contents/HandsOn_20251126.md
+course_contents/align_and_count_shell_script.md
 ```
 
 ```{toctree}
@@ -41,14 +42,6 @@ course_contents/HandsOn_20251126.md
 data/README.md
 ```
 
-```{toctree}
-:maxdepth: 2
-:hidden:
-:caption: scripts
-
-scripts/align_and_count_shell_script.md
-```
-
 ```{toctree}
 :maxdepth: 2
 :hidden: