From bdd309b073b6e836b78de28e82da89baba66a2a9 Mon Sep 17 00:00:00 2001 From: Peter Amstutz Date: Wed, 8 Oct 2014 15:00:42 -0400 Subject: [PATCH] Updated examples. --- .../_run_command_foreach_example.liquid | 28 ++++++++----------- .../topics/run-command.html.textile.liquid | 10 +++++++ 2 files changed, 22 insertions(+), 16 deletions(-) diff --git a/doc/_includes/_run_command_foreach_example.liquid b/doc/_includes/_run_command_foreach_example.liquid index 828499f51f..d5643e6410 100644 --- a/doc/_includes/_run_command_foreach_example.liquid +++ b/doc/_includes/_run_command_foreach_example.liquid @@ -15,25 +15,10 @@ { "foreach": "read_pair", "command": "$(read_pair)" - }, - "$(glob $(dir $(sample))/*_1.fastq)", - "$(glob $(dir $(sample))/*_2.fastq)" + } ], "task.stdout": "$(basename $(glob $(dir $(sample))/*_1.fastq)).sam", "task.foreach": ["sample_subdir", "read_pair"], - "reference_collection": "2463fa9efeb75e099685528b3b9071e0+438", - "samples": "df45f4be79668b6d3d974e24f78e766f+149", - "sample_subdir": "$(dir $(samples))", - "read_pair": { - "group": "sample_subdir", - "regex": "(.*)_[12]\\.fastq(\\.gz)?$" - } - } - } - } -} - - "reference_collection": { "required": true, "dataclass": "Collection" @@ -42,3 +27,14 @@ "required": true, "dataclass": "Collection" } + "sample_subdir": "$(dir $(samples))", + "read_pair": { + "value": { + "group": "sample_subdir", + "regex": "(.*)_[12]\\.fastq(\\.gz)?$" + } + } + } + } + } +} 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"] + +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. + +{% code 'run_command_simple_example' as javascript %} + +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. + +{% code 'run_command_foreach_example' as javascript %} -- 2.30.2