X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/e74cd2fb8d2863e3c40febd5b71a24a1bf945ec5..bdd309b073b6e836b78de28e82da89baba66a2a9:/doc/user/topics/run-command.html.textile.liquid

diff --git a/doc/user/topics/run-command.html.textile.liquid b/doc/user/topics/run-command.html.textile.liquid
index 078f4a33e7..dc4bc1fbc7 100644
--- a/doc/user/topics/run-command.html.textile.liquid
+++ b/doc/user/topics/run-command.html.textile.liquid
@@ -214,3 +214,13 @@ This evaluates to the commands:
 ["echo", "bob", "carol"]
 ["echo", "bob", "dave"]
 </pre>
+
+h1. Examples
+
+The following is a single task pipeline using run-command to run the bwa alignment tool to align a single paired-end read fastq sample.  The input to this pipeline is the reference genome and a collection consisting of two fastq files for the read pair.
+
+<notextile>{% code 'run_command_simple_example' as javascript %}</notextile>
+
+The following is a concurrent task pipeline using run-command to run the bwa alignment tool to align a set of fastq reads over multiple sample.  The input to this pipeline is the reference genome and a collection consisting subdirectories for each sample, with each subdirectory containing pairs of fastq files for each set of reads.
+
+<notextile>{% code 'run_command_foreach_example' as javascript %}</notextile>