added list of useful features

Workflow-management.md

@@ -65,8 +65,22 @@ rule sort_group_names:
         "only_users.txt",    # only contains the user names
     shell:
         "sort < {input[0]} | tee {output[0]} | cut -d ' ' -f 2 > {output[1]}"
+
+rule filter_by_letter:
+    input:
+        rules.list_groups_with_users.output[0]
+    output:
+        "start_with_letter_{letter}.txt", # only groups starting with a letter
+    shell:
+        "grep '^{wildcards.letter}' < {input} > {output}"
 ```
 
+> This example filters the file /etc/group (which contains all groups on a linux
+> system) and writes to three files. The first has the group name and users
+> (created by the first rule). Then the second rule creates a sorted file and a
+> file with the user names only. This rather pointless application shows that it
+> is possible to chain rule inputs and outputs, and to have multiple outputs.
+
 Executing the workflow with the command `snakemake only_users.txt` (to tell it
 to generate the `only_users.txt` file) should execute both rules, with an output
 similar to:
@@ -122,13 +136,38 @@ outputs (which are numbered from `0` to `N` by default, and can be named). The
 `shell` directive specifies that we want to run a shell command. This is the
 most flexible option. Alternatively one can use the `run` directive and write
 inline python code directly in the `Snakefile`, the `script` directive, which
-specifies the name of a Python (or another language) script to be run (Snakemake
-creates a context for this script which allows it to access the input and output
-objects), or finally the `notebook` directive, similar to the `script`
-directive, for which Snakemake allows interactive execution (useful for
-postprocessing/data exploration).
+specifies the name of a Python (or another language)
+[script](https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#external-scripts)
+to be run (Snakemake creates a context for this script which allows it to access
+the input and output objects), or finally the [`notebook`
+directive](https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#jupyter-notebook-integration),
+similar to the `script` directive, for which Snakemake allows interactive
+execution (useful for postprocessing/data exploration).
 
 Reading the
 [documentation](https://snakemake.readthedocs.io/en/stable/index.html) is highly
 recommended. Although the examples are often biology oriented, the features they
 demonstrate are easily transposed to a mechanics environment.
+
+Here is a list of useful features:
+
+- [Wildcards](https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#wildcards)
+  allow to specify parameter values from file names. In the example above,
+  running `snakemake start_with_letter_m.txt` will replace the
+  `{wildcards.letter}` in the `shell` directive by `m`. This is very useful to
+  distinguish output files based on parameter values. Multiple wildcards can be
+  used in the same rule.
+- [Expansion](https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#the-expand-function)
+  allows to specify a range of values for a wildcard. This is useful to explore
+  a parametric space, or
+  [aggregate](https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#defining-scatter-gather-processes)
+  the data of several values for one wildcard.
+- [Rule
+  parameters](https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules)
+  allow one to specify additional parameters (i.e. non-file inputs) to rules.
+- [Rule
+  dependencies](https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#rule-dependencies)
+  allow using the output of a rule as input to another without having to specify
+  the name.
+- [Parameter space
+  exploration](https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#parameter-space-exploration).