formatting

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

diff --git a/lesson3/lesson3.md b/lesson3/lesson3.md
index b7e333452f9613894aea5f372109e4ba6da21a3e..622f446ed5ecef7ab674b00dcbd766c251c19477 100644 (file)
--- a/lesson3/lesson3.md
+++ b/lesson3/lesson3.md
@@ -4,18 +4,18 @@ It is time to add the last step in the analysis.
 
 This will use the "featureCounts" tool from the "subread" package.
 
 
 This will use the "featureCounts" tool from the "subread" package.
 

-# Writing the tool wrapper
+### 1. File header

 
 

-1. Create a new file "featureCounts.cwl"
+Create a new file "featureCounts.cwl"

 
 

-2. Start with this header
+Start with this header

 
 ```
 cwlVersion: v1.2
 class: CommandLineTool
 ```
 
 
 ```
 cwlVersion: v1.2
 class: CommandLineTool
 ```
 

-3. Command line tool inputs
+### 2. Command line tool inputs

 
 A CommandLineTool describes a single invocation of a command line program.
 
 
 A CommandLineTool describes a single invocation of a command line program.
 


@@ -40,7 +40,7 @@ inputs:
   counts_input_bam: File
 ```
 
   counts_input_bam: File
 ```
 

-4. Specifying the program to run
+### 3. Specifying the program to run

 
 Give the name of the program to run in `baseCommand`.
 
 
 Give the name of the program to run in `baseCommand`.
 


@@ -48,7 +48,7 @@ Give the name of the program to run in `baseCommand`.
 baseCommand: featureCounts
 ```
 
 baseCommand: featureCounts
 ```
 

-5. Command arguments
+### 4. 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.
 
 The easiest way to describe the command line is with an `arguments`
 section.  This takes a comma-separated list of command line arguments.


@@ -68,7 +68,7 @@ arguments: [-T, $(runtime.cores),
                        $(inputs.counts_input_bam)]
 ```
 
                        $(inputs.counts_input_bam)]
 ```
 

-6. Outputs section
+### 5. Outputs section

 
 In CWL, you must explicitly identify the outputs of a program.  This
 associates output parameters with specific files, and enables the
 
 In CWL, you must explicitly identify the outputs of a program.  This
 associates output parameters with specific files, and enables the


@@ -93,7 +93,7 @@ outputs:
          glob: featurecounts.tsv
 ```
 
          glob: featurecounts.tsv
 ```
 

-7. Running in a container
+### 6. Running in a container

 
 In order to run the tool, it needs to be installed.
 Using software containers, a tool can be pre-installed into a
 
 In order to run the tool, it needs to be installed.
 Using software containers, a tool can be pre-installed into a


@@ -123,7 +123,7 @@ hints:
     dockerPull: quay.io/biocontainers/subread:1.5.0p3--0
 ```
 
     dockerPull: quay.io/biocontainers/subread:1.5.0p3--0
 ```
 

-8. Running a tool on its own
+### 7. Running a tool on its own

 
 When creating a tool wrapper, it is helpful to run it on its own to test it.
 
 
 When creating a tool wrapper, it is helpful to run it on its own to test it.
 


@@ -147,7 +147,7 @@ The invocation is also the same:
 cwl-runner featureCounts.cwl featureCounts.yaml
 ```
 
 cwl-runner featureCounts.cwl featureCounts.yaml
 ```
 

-9. Adding it to the workflow
+### 8. Adding it to the workflow

 
 Now that we have confirmed that it works, we can add it to our workflow.
 We add it to `steps`, connecting the output of samtools to
 
 Now that we have confirmed that it works, we can add it to our workflow.
 We add it to `steps`, connecting the output of samtools to

diff --git a/lesson4/lesson4.md b/lesson4/lesson4.md
index 447726d88bad9e48849a445f48fcf39e5178cd8c..6aa45de54b98f3ac44a585eb4bba587a6aa5a670 100644 (file)
--- a/lesson4/lesson4.md
+++ b/lesson4/lesson4.md
@@ -3,7 +3,7 @@
 Analyzing a single sample is great, but in the real world you probably
 have a batch of samples that you need to analyze and then compare.
 
 Analyzing a single sample is great, but in the real world you probably
 have a batch of samples that you need to analyze and then compare.
 

-1. Subworkflows
+### 1. Subworkflows

 
 In addition to running command line tools, a workflow step can also
 execute another workflow.
 
 In addition to running command line tools, a workflow step can also
 execute another workflow.


@@ -48,7 +48,7 @@ requirements:
 If you run this workflow, you will get exactly the same results as
 before, we've just wrapped the inner workflow with an outer workflow.
 
 If you run this workflow, you will get exactly the same results as
 before, we've just wrapped the inner workflow with an outer workflow.
 

-2. Scattering
+### 2. Scattering

 
 The wrapper lets us do something useful.  We can modify the outer
 workflow to accept a list of files, and then invoke the inner workflow
 
 The wrapper lets us do something useful.  We can modify the outer
 workflow to accept a list of files, and then invoke the inner workflow


@@ -104,7 +104,7 @@ requirements:
   ScatterFeatureRequirement: {}
 ```
 
   ScatterFeatureRequirement: {}
 ```
 

-3. Running with list inputs
+### 3. Running with list inputs

 
 The `fq` parameter needs to be a list.  You write a list in yaml by
 starting each list item with a dash.  Example `main-input.yaml`
 
 The `fq` parameter needs to be a list.  You write a list in yaml by
 starting each list item with a dash.  Example `main-input.yaml`


@@ -139,7 +139,7 @@ gtf:
 
 Now you can run the workflow the same way as in Lesson 2.
 
 
 Now you can run the workflow the same way as in Lesson 2.
 

-4. Combining results
+### 4. Combining results

 
 Each instance of the alignment workflow produces its own featureCounts
 file.  However, to be able to compare results easily, we need them a
 
 Each instance of the alignment workflow produces its own featureCounts
 file.  However, to be able to compare results easily, we need them a

diff --git a/lesson5/lesson5.md b/lesson5/lesson5.md
index 54df1348df4b8747970d7062db0454d968dabb0e..6a53398d940173d0e95659cdb0ac69547a647061 100644 (file)
--- a/lesson5/lesson5.md
+++ b/lesson5/lesson5.md
@@ -1,6 +1,6 @@
 # Expressions
 
 # Expressions
 

-1. Expressions on step inputs
+### 1. Expressions on step inputs

 
 You might have noticed that the output bam files are all named
 `Aligned.sortedByCoord.out.bam`.  This happens because because when we
 
 You might have noticed that the output bam files are all named
 `Aligned.sortedByCoord.out.bam`.  This happens because because when we


@@ -53,7 +53,7 @@ adds the remainder of the string, which just is a dot `.`.  This is to
 separate the leading part of our filename from the "Aligned.bam"
 extension that will be added by STAR.
 
 separate the leading part of our filename from the "Aligned.bam"
 extension that will be added by STAR.
 

-2. Organizing output files into Directories
+### 2. Organizing output files into Directories

 
 You probably noticed that all the output files appear in the same
 directory.  You might prefer that each file appears in its own
 
 You probably noticed that all the output files appear in the same
 directory.  You might prefer that each file appears in its own


@@ -139,7 +139,3 @@ outputs:
     type: File
     outputSource: featureCounts/featurecounts
 ```
     type: File
     outputSource: featureCounts/featurecounts
 ```

-
-3. Other uses for expressions
-
-- Creating configuration files on the fly.