Update awk.md

docs/workshops_courses/awk.md

@@ -23,37 +23,40 @@ Application: form.
 
 ## Schedule
 
-1-st day 9:15 - 12:00
+### 1-st day 9:15 - 12:00
 Seminar session
-Examples of typical problems suitable for Awk “treatment”
-Introduction to the basics of Awk scripting language
-Solving interactively simple problems
+  - Examples of typical problems suitable for Awk “treatment”
+  - Introduction to the basics of Awk scripting language
+  - Solving interactively simple problems
+
 Lunch break
-Exercises 13:15 -16:00
-Solving interactively the exercise problems
-2-nd day 9:15 - 12:00
-Awk for bioinformaticians - seminar
-Case Study: Manipulating the output from a genome analysis - vcf and gff
-Filtering and formatting raw data
-Counting and piling features
-Indexing and hashing to compare variants and annotations
+  - Exercises 13:15 -16:00
+  - Solving interactively the exercise problems
+
+### 2-nd day 9:15 - 12:00
+  - Awk for bioinformaticians - seminar
+  -  Case Study: Manipulating the output from a genome analysis - vcf and gff
+  -  Filtering and formatting raw data
+  -  Counting and piling features
+  - Indexing and hashing to compare variants and annotations
+
 Lunch break
-Walk-through session on various topics:
-Awk parsing “simultaneously” multiple input files
-Multiple input files - second approach scenario will be discussed.
-How to trick awk to accept options on the command line like regular program i.e. $ script.awk filename parameter1 parameter2 link
-Declaring and calling functions in awk - link
-Input/output to/from an external programs
-Learn how to send input to an external program (might be based on your data) and read the result back - link
-Handy tips: awk oneliners use with Vim, gnuplot…
+  - Walk-through session on various topics:
+  - Awk parsing “simultaneously” multiple input files
+  - Multiple input files - second approach scenario will be discussed.
+  - How to trick awk to accept options on the command line like regular program i.e. $ script.awk filename parameter1 parameter2 link
+  - Declaring and calling functions in awk - link
+  - Input/output to/from an external programs
+  - Learn how to send input to an external program (might be based on your data) and read the result back - link
+  - Handy tips: awk oneliners use with Vim, gnuplot…
 Also: Suggest topic for discussion or see recently suggested topics.
 
 ## Prerequisites
 
 ### MacOS
 The system provided awk version will work for most of the examples during the workshop with few exceptions, which are noted in the online material.
 
-Tilda ~ sign on Mac with Swedish keyboard layout - Alt + ^
+Tilda `~` sign on Mac with Swedish keyboard layout - Alt + ^
 
 ### Linux
 
@@ -62,7 +65,9 @@ Several distributions have other awk flavors installed by default. The easiest f
 ### Windows 10
 
 Ubuntu for Windows 10 - it is better to read from the source, despite it might not be the easiest tutorial. To my experience, this is the best Linux environment without virtualization.
+
 MobaXterm use the internal package manager to install gawk. The default is provided by Busybox and is not enough for the purpose of the workshop.
+
 Linux computer center
 Just login to your account and use the provided awk - any version newer than 4 will work.
 rackham3:[~] awk -V GNU Awk 4.0.2 Copyright (C) 1989, 1991-2012 Free Software Foundation.
@@ -73,30 +78,29 @@ Just follow some tutorial on how to setup and use the virtual Linux environment.
 
 ### VirtualBox
 
-Ubuntu on Public Clouds
-GitHub & Binder (you need only a browser)
-Singularity
-singularity run shub://pmitev/Teoroo-singularity:gawk 'BEGIN{ for(i=1;i<=4;i++) print i}'
+- Ubuntu on Public Clouds
+- GitHub & Binder (you need only a browser)
+- Singularity `singularity run shub://pmitev/Teoroo-singularity:gawk 'BEGIN{ for(i=1;i<=4;i++) print i}'`
 
 ## Feedback from previous workshops:
 
-2024.08 | 2024.01
-2023.09 | 2023.01*
-2022.09 | 2022.01
-​2021.09 | 2021.01
-2020.08 | 2020.01
-2019.08 | 2019.01
-2018.08 | 2018.01
-2017.01 | 2017.08
-2016.08 | 2016.01
-2015.10
+2024.08 | 2024.01  
+2023.09 | 2023.01*  
+2022.09 | 2022.01  
+​2021.09 | 2021.01  
+2020.08 | 2020.01  
+2019.08 | 2019.01  
+2018.08 | 2018.01  
+2017.01 | 2017.08  
+2016.08 | 2016.01  
+2015.10  
 * not enough data to be anonymous
 
 ## Contacts for the course:
 
-Pavlin Mitev
-Jonas Söderberg
-Lars Eklund
-Richel Bilderbeek
-UPPMAX
+Pavlin Mitev  
+Jonas Söderberg  
+Lars Eklund  
+Richel Bilderbeek  
+UPPMAX