Custom IO docs

Author: samirelanduk

README.rst

@@ -144,6 +144,24 @@ Once the run command string has been passed to the runner, nextflow.py will
 wait for the pipeline to complete by watching the execution directory, and then
 return the ``Execution`` object as normal.
 
+Custom IO
+~~~~~~~~~
+
+By default, nextflow will try to access the local filesystem when checking the
+output pipeline files. If you need to define alternative ways of doing this, you
+can create a custom ``IO`` object and pass it in as the ``io`` parameter to the
+``run`` method:
+
+    >>> execution = pipeline.run("my-pipeline.nf", io=my_custom_io)
+
+This object must define the following methods:
+
+* ``abspath(path)`` - Return the absolute path to a file.
+* ``listdir(path)`` - List the contents of a directory.
+* ``read(path, mode="r")`` - Read the contents of a file.
+* ``glob(path)`` - Glob a path.
+* ``ctime(path)`` - Get the creation time of a file.
+
 Polling
 ~~~~~~~
 

docs/source/overview.rst

@@ -64,6 +64,24 @@ Once the run command string has been passed to the runner, nextflow.py will
 wait for the pipeline to complete by watching the execution directory, and then
 return the :py:class:`.Execution` object as normal.
 
+Custom IO
+~~~~~~~~~
+
+By default, nextflow will try to access the local filesystem when checking the
+output pipeline files. If you need to define alternative ways of doing this, you
+can create a custom ``IO`` object and pass it in as the ``io`` parameter to the
+``run`` method:
+
+    >>> execution = pipeline.run("my-pipeline.nf", io=my_custom_io)
+
+This object must define the following methods:
+
+* ``abspath(path)`` - Return the absolute path to a file.
+* ``listdir(path)`` - List the contents of a directory.
+* ``read(path, mode="r")`` - Read the contents of a file.
+* ``glob(path)`` - Glob a path.
+* ``ctime(path)`` - Get the creation time of a file.
+
 Polling
 ~~~~~~~
 

nextflow/io.py

@@ -60,29 +60,4 @@ def get_process_ids_to_paths(process_ids, execution_path, io=None):
             if sub.startswith(process_id):
                 process_ids_to_paths[process_id] = subdirectory
                 break
-    return process_ids_to_paths
-
-
-
-
-class CustomIO:
-
-    def abspath(path):
-        pass
-
-
-    def listdir(path):
-        pass
-
-
-    def read(path, mode="r"):
-        pass
-
-
-    def ctime(path):
-        pass
-
-
-    def glob(path):
-        pass
-    
+    return process_ids_to_paths