Fix broken links and formatting in README

README.md

@@ -10,22 +10,33 @@
 
 __Microbial Sequence Analysis and Loci-based Typing pipeline__
 
-_The microbial sequence analysis and loci-based typing pipeline (microSALT) is used to analyse microbial samples.
-It produces a quality control of the sample, determines a sample's organism specific sequence type, and its resistance pattern. microSALT also provides a database storage solution and report generation of these results._
+_The microbial sequence analysis and loci-based typing pipeline (microSALT) is
+used to analyse microbial samples.  It produces a quality control of the
+sample, determines a sample's organism specific sequence type, and its
+resistance pattern. microSALT also provides a database storage solution and
+report generation of these results._
 
-_microSALT uses a combination of python, sqLite and flask. Python is used for the majority of functionality, the database is handled through sqLite and the front-end is handled through flask. All analysis activity by microSALT requires a SLURM cluster._
+_microSALT uses a combination of python, sqLite and flask. Python is used for
+the majority of functionality, the database is handled through sqLite and the
+front-end is handled through flask. All analysis activity by microSALT requires
+a SLURM cluster._
 
 ## Quick installation
-* `yes | bash <(curl https://raw.githubusercontent.com/Clinical-Genomics/microSALT/master/install.sh)`
-* `cp configExample.json $HOME/.microSALT/config.json`
-* `vim $HOME/.microSALT/config.json`
+
+1. `yes | bash <(curl https://raw.githubusercontent.com/Clinical-Genomics/microSALT/master/install.sh)`
+2. `cp configExample.json $HOME/.microSALT/config.json`
+3. `vim $HOME/.microSALT/config.json`
 
 ## Configuration
-Copy the configuration file to microSALTs hidden home directory, _or_ copy the configuration file anywhere and direct the envvar MICROSALT_CONFIG to it. See example: 
+
+Copy the configuration file to microSALTs hidden home directory, _or_ copy the
+configuration file anywhere and direct the envvar MICROSALT_CONFIG to it. See
+example:
 
 `cp configExample.json $HOME/.microSALT/config.json`
 
 _or_
+
 ```
 cp configExample.json /MY/FAV/FOLDER/config.json
 export MICROSALT_CONFIG=/MY/FAV/FOLDER/config.json
@@ -34,35 +45,49 @@ export MICROSALT_CONFIG=/MY/FAV/FOLDER/config.json
 __Then edit the fields to match your environment__.
 
 ## Usage
-* `microSALT analyse` contains functions to start sbatch job(s) & produce output to `folders['results']`. Afterwards the parsed results  are uploaded to the SQL back-end and produce reports (HTML), which are then automatically e-mailed to the user.
-* `microSALT utils` contains various functionality, including generating the sample description json, manually adding new reference organisms and re-generating reports.
+
+- `microSALT analyse` contains functions to start sbatch job(s) & produce
+  output to `folders['results']`. Afterwards the parsed results  are uploaded
+  to the SQL back-end and produce reports (HTML), which are then automatically
+  e-mailed to the user.
+- `microSALT utils` contains various functionality, including generating the
+  sample description json, manually adding new reference organisms and
+  re-generating reports.
 
 ## Databases
+
 ### MLST Definitions
-microSALT will automatically download & use the MLST definitions for any organism on pubMLST (https://pubmlst.org/databases/).
-Other definitions may be used, as long as they retain the same format. 
+
+microSALT will automatically download & use the MLST definitions for any
+organism on [pubMLST](https://pubmlst.org/databases). Other definitions may be
+used, as long as they retain the same format.
 
 ### Resistance genes
-microSALT will automatically download & use the resistance genes of resFinder (https://cge.cbs.dtu.dk/services/data.php).
+
+microSALT will automatically download & use the resistance genes of [ResFinder](https://bitbucket.org/genomicepidemiology/resfinder).
 Any definitions will work, as long as they retain the same formatting.
 
 ## Requirements
+
 ### Hardware
-* A slurm enabled HPC
-* A (clarity) LIMS server
 
+- A [SLURM](https://slurm.schedmd.com) enabled HPC system
+- A (clarity) LIMS server
 
 ### Software
-* Conda ( https://www.anaconda.com/distribution/ )
-* Python 3.6
-* sqLite Service ( https://www.sqlite.org/download.html )
+
+- [Conda](https://conda.io)
+- Python 3.6
+- [SQLite](https://www.sqlite.org)
 
 ## Contributing to this repo
+
 This repository follows the Github flow approach to adding updates.
 For more information, see https://guides.github.com/introduction/flow/
 
 ## Credits
-* Isak Sylvin - Lead developer
-* Emma Sernstad - Accreditation ready reports
-* Tanja Normark - Various issues
-* Maya Brandi - Various issues
+
+- Isak Sylvin - Lead developer
+- Emma Sernstad - Accreditation ready reports
+- Tanja Normark - Various issues
+- Maya Brandi - Various issues