change screen to index

.gitlab-ci.yml

@@ -27,7 +27,7 @@ i-cl:
 i-with-another-filter:
     stage: init
     script:
-        - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db init --screen $CI_PROJECT_DIR/test/small.fa
+        - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db init --index $CI_PROJECT_DIR/test/small.fa
 
 
 

impy.py

@@ -362,9 +362,9 @@ def get_members(tar, prefix):
 
 @cli.command()
 @click.option('--generate', default=False, is_flag=True, help='Download and process the databases from original tools.')
-@click.option('--screen', help='Fasta file path to use for filtering.')
+@click.option('--index', help='Fasta file path to use for filtering.')
 @click.pass_context
-def init(ctx, generate, screen):
+def init(ctx, generate, index):
     """
     Initialise databases.
     The initialisation is in two steps:
@@ -381,7 +381,7 @@ def init(ctx, generate, screen):
     ev = {}
 
     # check if fasta file is provided
-    if screen:
+    if index:
         screen_path = Path(screen).abspath()
         if not screen_path.exists():
             click.secho('Path provided does not exist: `%s`.' % screen_path, fg='red', bold=True)

setup.py

@@ -10,7 +10,7 @@ def read(fname):
 
 setup(
     name='impy',
-    version='0.2.4',
+    version='0.2.5',
     author="Shaman Narayanasamy, Yohan Jarosz",
     author_email="shaman.narayanasamy@uni.lu, yohan.jarosz@uni.lu",
     description=("Integrated Metaomic Pipeline command-line utility."),