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docs: polish
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johanneskoester committed Sep 21, 2021
1 parent 5111150 commit 47a7b628686258a28dd870f20bf1f121b3a881c3
Showing 1 changed file with 4 additions and 4 deletions.
@@ -237,10 +237,6 @@ For sorting, ``samtools`` requires a prefix specified with the flag ``-T``.
Here, we need the value of the wildcard ``sample``.
Snakemake allows to access wildcards in the shell command via the ``wildcards`` object that has an attribute with the value for each wildcard.

.. sidebar:: Note

It is best practice to have subsequent steps of a workflow in separate, unique, output folders. This keeps the working directory structured. Further, such unique prefixes allow Snakemake to quickly discard most rules in its search for rules that can provide the requested input. This accelerates the resolution of the rule dependencies in a workflow.

When issuing

.. code:: console
@@ -250,6 +246,10 @@ When issuing
you will see how Snakemake wants to run first the rule ``bwa_map`` and then the rule ``samtools_sort`` to create the desired target file:
as mentioned before, the dependencies are resolved automatically by matching file names.

.. sidebar:: Note

It is best practice to have subsequent steps of a workflow in separate, unique, output folders. This keeps the working directory structured. Further, such unique prefixes allow Snakemake to quickly discard most rules in its search for rules that can provide the requested input. This accelerates the resolution of the rule dependencies in a workflow.

Step 4: Indexing read alignments and visualizing the DAG of jobs
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