From: Peter Amstutz <peter.amstutz@curii.com>
Date: Tue, 19 Jan 2021 23:01:28 +0000 (-0500)
Subject: Still working on it.
X-Git-Url: https://git.arvados.org/rnaseq-cwl-training.git/commitdiff_plain/1b451366891e7fddcb408e5ae7a6a741292cdeee

Still working on it.

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
---

diff --git a/lesson1/lesson1.md b/lesson1/lesson1.md
index 060597a..4846d72 100644
--- a/lesson1/lesson1.md
+++ b/lesson1/lesson1.md
@@ -54,7 +54,18 @@ series of steps, and produce output values.
 
 For this analysis, the input parameters are the fastq file and the reference data required by STAR.
 
-In CWL, these are declared in the `inputs` section.
+In the original bash script, the following variables are declared:
+
+```
+# initialize a variable with an intuitive name to store the name of the input fastq file
+fq=$1
+
+# directory with genome reference FASTA and index files + name of the gene annotation file
+genome=rnaseq/reference_data
+gtf=rnaseq/reference_data/chr1-hg19_genes.gtf
+```
+
+In CWL, we will declare these variables in the `inputs` section.
 
 The inputs section lists each input parameter and its type.  Valid
 types include `File`, `Directory`, `string`, `boolean`, `int`, and
diff --git a/lesson2/lesson2.md b/lesson2/lesson2.md
index a5ec6a7..02bedfb 100644
--- a/lesson2/lesson2.md
+++ b/lesson2/lesson2.md
@@ -118,7 +118,7 @@ After setting the RAM requirements, re-run the workflow.
 
 5. Workflow results
 
-The CWL runner will print a results JSON object.  It will look something like this (it may include additional fields).
+The CWL runner will print a results JSON object to standard output.  It will look something like this (it may include additional fields).
 
 
 ```
diff --git a/lesson3/lesson3.md b/lesson3/lesson3.md
new file mode 100644
index 0000000..93e9a55
--- /dev/null
+++ b/lesson3/lesson3.md
@@ -0,0 +1,120 @@
+# Writing a tool wrapper
+
+It is time to add the last step in the analysis.
+
+This will use the "featureCounts" tool from the "subread" package.
+
+# Writing the tool wrapper
+
+1. Create a new file "featureCounts.cwl"
+
+2. Start with this header
+
+```
+cwlVersion: v1.2
+class: CommandLineTool
+```
+
+3. Command line tool inputs
+
+A CommandLineTool describes a single invocation of a command line program.
+
+It consumes some input parameters, runs a program, and produce output
+values.
+
+Here's the original bash script
+
+```
+featureCounts -T $cores -s 2 -a $gtf -o $counts $counts_input_bam
+```
+
+The variables used in the bash script are `$cores`, `$gtf`, `$counts` and `$counts_input_bam`.
+
+The parameters
+
+This gives us two file inputs, `gtf` and `counts_input_bam` which we can declare in our `inputs` section:
+
+```
+inputs:
+  gtf: File
+  counts_input_bam: File
+```
+
+4. The base command
+
+This one is easy.  This is the name of program to run:
+
+```
+baseCommand: featureCounts
+```
+
+5. The command arguments
+
+The easiest way to describe the command line is with an `arguments`
+section.  This takes a comma-separated list of command line arguments.
+
+Input variables are included on the command line as
+`$(inputs.name_of_parameter)`.  When the tool is executed, these input
+parameter values are substituted for these variable.
+
+Special variables are also available.  The runtime environment
+describes the resources allocated to running the program.  Here we use
+`$(runtime.cores)` to decide how many threads to request.
+
+File variables can also yield a partial filename, by adding
+`.nameroot`.  This is the filename with the final dot-extension
+stripped off.
+
+```
+arguments: [-T, $(runtime.cores),
+            -a, $(inputs.gtf),
+			-o, $(inputs.counts_input_bam.nameroot)_featurecounts.txt,
+			$(inputs.counts_input_bam)]
+```
+
+6. The outputs section
+
+In CWL, you must explicitly identify the outputs of a program.  This
+associates output parameters with specific files, and allows the
+workflow runner to know which files must be saved and which files can
+be discarded.
+
+In the previous section, we told the featureCounts program the name of
+our output files should be
+`$(inputs.counts_input_bam.nameroot)_featurecounts.txt`.
+
+We can declare an output parameter called `featurecounts` that will
+have that output file as its value.
+
+The `outputBinding` section describes how to determine the value of
+the parameter.  The `glob` field tells it to search for a file in the
+output directory with the
+`$(inputs.counts_input_bam.nameroot)_featurecounts.txt`
+
+```
+outputs:
+  featurecounts:
+    type: File
+	outputBinding:
+	  glob: $(inputs.counts_input_bam.nameroot)_featurecounts.txt
+```
+
+N.
+
+The most portable way to run a tool is to wrap it in a Docker
+container.  (Some CWL platforms, such as Arvados, require it).  Many
+bioinformatics tools are already available as containers.  One
+resource is the BioContainers project.
+
+Visit https://biocontainers.pro/
+
+Click on "Registry"
+
+Search for "subread"
+
+Click on the search result for "subread"
+
+Click on the tab "Packages and Containers"
+
+Choose a row with type "docker", then click the "copy to clipboard"
+button on the right side of the"Full Tag" column for that row.