corrected missedCleavages key

wilhelm-lab · Oct 6, 2023 · bfce8db · bfce8db
1 parent 9fc0ea2
commit bfce8db
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Showing 3 changed files with 7 additions and 7 deletions.
diff --git a/README.rst b/README.rst
@@ -65,7 +65,7 @@ Prerequisites:
   - `docker <https://www.docker.com/>`_
 
 After cloning the repository of oktoberfest, checkout the branch you want to build the container from.
-The latest stable version is always on the main branch.
+The latest stable version is always on the main branch. Then build the container.
 
 .. code-block:: bash
 
@@ -150,7 +150,7 @@ The following flags are relevant only if a FASTA file is provided:
 - `fastaDigestOptions`
    - `fragmentation` = fragmentation method: "HCD" or "CID"
    - `digestion` = digestion mode: "full", "semi" or None; default = "full"
-   - `cleavages` = number of allowed missed cleavages used in the search engine; default = 2
+   - `missedCleavages` = number of allowed missed cleavages used in the search engine; default = 2
    - `minLength` = minimum peptide length allowed used in the search engine; default = 7
    - `maxLength` = maximum peptide length allowed used in the search engine; default = 60
    - `enzyme` = type of enzyme used in the search engine; default = "trypsin"
@@ -166,7 +166,7 @@ The general command for executing any job is:
 
 .. code-block:: bash
 
-   python oktoberfest/run_oktoberfest.py --config_path path_to_config_file
+   python -m oktoberfest --config_path path_to_config_file
 
 If you instead want to run oktoberfest using the docker image, run:
 

diff --git a/ReadMe.md b/ReadMe.md
@@ -39,7 +39,7 @@ Prerequisites:
 -   `docker` (https://www.docker.com/)
 
 After cloning the repository of oktoberfest, checkout the branch you want to build the container from.
-The latest stable version is always on the main branch.
+The latest stable version is always on the main branch. Then build the container.
 
 ```bash
 make build
@@ -147,7 +147,7 @@ The following flags are relevant only if a FASTA file is provided:
 
     -   `digestion` = digestion mode: "full", "semi" or None; default = "full"
 
-    -   `cleavages` = number of allowed missed cleavages used in the search engine; default = 2
+    -   `missedCleavages` = number of allowed missed cleavages used in the search engine; default = 2
 
     -   `minLength` = minimum peptide length allowed used in the search engine; default = 7
 
@@ -166,7 +166,7 @@ An example of the config file can be found in `/oktoberfest/example_config.json`
 The general command for executing any job is:
 
 ```bash
-python oktoberfest/run_oktoberfest.py --config_path path_to_config_file
+python -m oktoberfest --config_path path_to_config_file
 ```
 
 If you instead want to run oktoberfest using the docker image, run:

diff --git a/docs/config.rst b/docs/config.rst
@@ -90,7 +90,7 @@ Additional parameters required for in-silico digestion
    +----------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------+
    |     digestion              | Digestion mode; can be "full", "semi" or None; default = "full"                                                                                                    |
    +----------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-   |     cleavages              | Number of allowed missed cleavages used in the search engine for generation of the provided search results; default = 2                                            |
+   |     missedCleavages        | Number of allowed missed cleavages used in the search engine for generation of the provided search results; default = 2                                            |
    +----------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------+
    |     minLength              | Minimum peptide length allowed used in the search engine for generation of the provided search results; default = 7                                                |
    +----------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------+