small changes #7

README.md

@@ -13,7 +13,7 @@
 
 SPECIMEN is a collection of different workflows designed for the automated and standardised curation of genome-scale models. It is mainly based on the [refineGEMs toolbox](https://github.com/draeger-lab/refinegems/tree/dev-2), but also includes additional tools like [CarveMe](https://carveme.readthedocs.io/en/latest/).
 
-> Note: This tool is currently still under active developement, any feedback or ides are welcome.
+> Note: This tool is currently still under active developement, any feedback or ideas are welcome.
 
 Currently avaible workflow:
 

docs/source/cmpb/run-pipeline.rst

@@ -57,7 +57,10 @@ from inside a Python script or Jupyter Notebook with "config.yaml" being the pat
 
 The pipeline has two obligatory parameters:
 
-- The path to the annotated genome file (if a model is given, should be the file used to create it)
+- Path to a model 
+
+    - If no model is given, the `protein_fasta` needs to be provided. The format needs to be the same as the files provides by NCBI under `<GenBank assembly>` -> `ftp` -> `<name>_translated_cds.faa.gz`
+
 - A media configuration (from refineGEMs) for testing the model's growth
 
 Further data can be added as available and/or needed (all are completely optional):

pyproject.toml

@@ -49,7 +49,6 @@ docs = ["accessible-pygments",
        "sphinx_copybutton",
        "pip-tools"]
 
-# @TODO:
 [project.urls]
 repository = 'https://github.com/draeger-lab/SPECIMEN'
 documentation = 'https://specimen.readthedocs.io/en/latest/'

src/specimen/data/config/cmpb_config.yaml

@@ -15,7 +15,7 @@
 input:
   modelpath: NULL            # Optional, path to a model.
                              # If not given, runs CarveMe -> Future update!
-  annotated_genome: __USER__ # Required, path to the annotated genome file
+  # annotated_genome: USER # Some alternative input if not model is given
   mediapath: __USER__        # Path to a media config to test growth with
 
 # General options
@@ -46,6 +46,7 @@ cm-polish:
   email: USER              # User Mail to use for Entrez 
   protein_fasta: USER      # Optional, except for 'is_lab_strain: True'.
                            # The path to the protein FASTA used to create the CarveMe model.
+                           # For more information, please refer to the documentation.
   is_lab_strain: False     # Whether the users strain originates from a lab
                            # Needs to be set to ensure that protein IDs get the 'bqbiol:isHomologTo' qualifier
                            # & to set the locus_tag to the ones obtained by the annotation