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Formatting
[rnaseq-cwl-training.git]
/
lesson1
/
lesson1.md
diff --git
a/lesson1/lesson1.md
b/lesson1/lesson1.md
index b989855ab8f7811e8c35e2dd823cbd9782ef21e7..f394c901f82c5583152839a31975ddfcf1eae3ac 100644
(file)
--- a/
lesson1/lesson1.md
+++ b/
lesson1/lesson1.md
@@
-2,7
+2,7
@@
In this lesson we will turn `rnaseq_analysis_on_input_file.sh` into a workflow.
In this lesson we will turn `rnaseq_analysis_on_input_file.sh` into a workflow.
-# Setting up
+#
#
Setting up
We will create a new git repository and import a library of existing
tool definitions that will help us build our workflow.
We will create a new git repository and import a library of existing
tool definitions that will help us build our workflow.
@@
-11,19
+11,16
@@
tool definitions that will help us build our workflow.
2. Create a new git repository to hold our workflow with this command:
2. Create a new git repository to hold our workflow with this command:
-## Arvados
-
```
```
-git
clone https://github.com/arvados/arvados-vscode-cwl-template.g
it rnaseq-cwl-training-exercises
+git
in
it rnaseq-cwl-training-exercises
```
```
-## Generic
+On Arvados use this:
```
```
-git
in
it rnaseq-cwl-training-exercises
+git
clone https://github.com/arvados/arvados-vscode-cwl-template.g
it rnaseq-cwl-training-exercises
```
```
-
3. Go to File->Open Folder and select rnaseq-cwl-training-exercises
4. Go to the terminal window
3. Go to File->Open Folder and select rnaseq-cwl-training-exercises
4. Go to the terminal window
@@
-34,11
+31,13
@@
git init rnaseq-cwl-training-exercises
git submodule add https://github.com/common-workflow-library/bio-cwl-tools.git
```
git submodule add https://github.com/common-workflow-library/bio-cwl-tools.git
```
-# Writing the workflow
+## Writing the workflow
+
+### 1. File header
-
1.
Create a new file "main.cwl"
+Create a new file "main.cwl"
-
2.
Start with this header.
+Start with this header.
```
```
@@
-47,7
+46,7
@@
class: Workflow
label: RNAseq CWL practice workflow
```
label: RNAseq CWL practice workflow
```
-
3
. Workflow Inputs
+
### 2
. Workflow Inputs
The purpose of a workflow is to consume some input parameters, run a
series of steps, and produce output values.
The purpose of a workflow is to consume some input parameters, run a
series of steps, and produce output values.
@@
-80,7
+79,7
@@
inputs:
gtf: File
```
gtf: File
```
-
4
. Workflow Steps
+
### 3
. Workflow Steps
A workflow consists of one or more steps. This is the `steps` section.
A workflow consists of one or more steps. This is the `steps` section.
@@
-115,7
+114,7
@@
steps:
out: [html_file]
```
out: [html_file]
```
-
5
. Running alignment with STAR
+
### 4
. Running alignment with STAR
STAR has more parameters. Sometimes we want to provide input values
to a step without making them as workflow-level inputs. We can do
STAR has more parameters. Sometimes we want to provide input values
to a step without making them as workflow-level inputs. We can do
@@
-137,7
+136,7
@@
this with `{default: N}`
out: [alignment]
```
out: [alignment]
```
-
6
. Running samtools
+
### 5
. Running samtools
The third step is to generate an index for the aligned BAM.
The third step is to generate an index for the aligned BAM.
@@
-156,7
+155,7
@@
step will not run until the `STAR` step has completed successfully.
out: [bam_sorted_indexed]
```
out: [bam_sorted_indexed]
```
-
7
. featureCounts
+
### 6
. featureCounts
As of this writing, the `subread` package that provides
`featureCounts` is not available in bio-cwl-tools (and if it has been
As of this writing, the `subread` package that provides
`featureCounts` is not available in bio-cwl-tools (and if it has been
@@
-164,7
+163,7
@@
added since writing this, let's pretend that it isn't there.) We will
dive into how to write a CWL wrapper for a command line tool in
lesson 2. For now, we will leave off the final step.
dive into how to write a CWL wrapper for a command line tool in
lesson 2. For now, we will leave off the final step.
-
8
. Workflow Outputs
+
### 7
. Workflow Outputs
The last thing to do is declare the workflow outputs in the `outputs` section.
The last thing to do is declare the workflow outputs in the `outputs` section.