Update documentation

Added bitia-cli docs info

docs/source/getting_started/Working.md

@@ -3,6 +3,11 @@ BiTIA has two commands to work on it:
 - run
 - submit
 
+## run
+```{eval-rst}
+.. autofunction:: bitia.__main__.prepare_archive
+```
+
 ### Bitia run can be employed in three ways;
 
 #### Example 1 - Input as String

docs/source/index.md

@@ -45,6 +45,7 @@ getting_started/Working
 
 If you want to learn how to use BiTIA and installation, check out the following resources:
 
+<<<<<<< HEAD
 <details >
 <summary><b>REQUIREMENTS</b></summary>
 
@@ -117,6 +118,10 @@ NGS bioinformatics pipelines are frequently platform specific and may be customi
 > Sequence generation (signal processing and base calling) is the process that converts sensor (optical and nonoptical) data from the sequencing platform and identifies the sequence of nucleotides for each of the short fragments of DNA in the sample prepared for analysis. For each nucleotide sequenced in these short fragments (ie, raw reads), a corresponding Phred-like quality score is assigned, which is sequencing platform specific. The read sequences along with the Phred-like quality scores are stored in a FASTQ file, which is a de facto standard for representing biological sequence information
 </details>
 
+=======
+- [Installation](getting_started/Installation.md) 
+- [Working with BiTIA](getting_started/Working.md)
+>>>>>>> 483a0a9 (Added bitia-cli docs info)
 
 
 <details>
@@ -170,6 +175,10 @@ $ bitia run bitia.main.sh
 <!-- 
 ```{eval-rst}
 .. automodule:: bitia
+<<<<<<< HEAD
 ``` -->
+=======
+```
+>>>>>>> 483a0a9 (Added bitia-cli docs info)