Merge pull request #238 from Clinical-Genomics/feat/rename-cli-to-microsalt

Rename CLI entry point from microSALT to microsalt

Author: karlnyr

README.md

@@ -49,11 +49,11 @@ export MICROSALT_CONFIG=/MY/FAV/FOLDER/config.json
 
 ## Usage
 
-- `microSALT analyse` contains functions to start sbatch job(s) & produce
+- `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
+- `microsalt utils` contains various functionality, including generating the
   sample description json, manually adding new reference organisms and
   re-generating reports.
 

microSALT/utils/job_creator.py

@@ -684,7 +684,7 @@ def finish_job(self, joblist, single_sample=False):
                 mb.write(f"export MICROSALT_CONFIG={os.environ['MICROSALT_CONFIG']}\n")
             conda_cmd = (
                 f"conda run -p {os.environ['CONDA_PREFIX']} "
-                f"microSALT utils finish {self.finishdir}/sampleinfo.json "
+                f"microsalt utils finish {self.finishdir}/sampleinfo.json "
                 f"--input {self.finishdir} "
                 f"--email {self.regex.mail_recipient} "
                 f"--report {report} "

pyproject.toml

@@ -25,7 +25,7 @@ dependencies = [
 ]
 
 [project.scripts]
-microSALT = "microSALT.cli:root"
+microsalt = "microSALT.cli:root"
 
 [project.urls]
 Homepage = "https://github.com/Clinical-Genomics/microSALT"