-# Turning a bash script into a workflow
+# Turning a bash script into a workflow using existing tools
In this lesson we will turn `rnaseq_analysis_on_input_file.sh` into a workflow.
+
+# Setting up
+
+We will create a new git repository and import a library of existing
+tool definitions that will help us build our workflow.
+
+1. Select "Terminal->New terminal"
+
+2. Create a new git repository to hold our workflow with this command:
+
+## Arvados
+
+```
+git clone https://github.com/arvados/arvados-vscode-cwl-template.git rnaseq-cwl-training-exercises
+```
+
+## Generic
+
+```
+git init rnaseq-cwl-training-exercises
+```
+
+
+3. Go to File->Open Folder and select rnaseq-cwl-training-exercises
+
+4. Go to the terminal window
+
+5. Import bio-cwl-tools with this command:
+
+```
+git submodule add https://github.com/common-workflow-library/bio-cwl-tools.git
+```
+
+# Writing the workflow
+
+1. Create a new file "main.cwl"
+
+2. Start with this header.
+
+
+```
+cwlVersion: v1.2
+class: Workflow
+label: RNAseq CWL practice workflow
+```
+
+3. Workflow Inputs
+
+The purpose of a workflow is to consume some input parameters, run a
+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.
+
+The inputs section lists each input parameter and its type. Valid
+types include `File`, `Directory`, `string`, `boolean`, `int`, and
+`float`.
+
+In this case, the fastq and gene annotation file are individual files. The STAR index is a directory. We can describe these inputs in CWL like this:
+
+```
+inputs:
+ fq: File
+ genome: Directory
+ gtf: File
+```
+
+4. Workflow Steps
+
+A workflow consists of one or more steps. This is the `steps` section.
+
+Now we need to describe the first step of the workflow. This step is to run `fastqc`.
+
+A workflow step consists of the name of the step, the tool to `run`,
+the input parameters to be passed to the tool in `in`, and the output
+parameters expected from the tool in `out`.
+
+The value of `run` references the tool file. Tip: while typing the
+file name, you can get suggestions and auto-completion on a partial
+name using control+space.
+
+The `in` block lists input parameters to the tool and the workflow
+parameters that will be assigned to those inputs.
+
+The `out` block lists output parameters to the tool that are used
+later in the workflow.
+
+You need to know which input and output parameters are available for
+each tool. In vscode, click on the value of `run` and select "Go to
+definition" to open the tool file. Look for the `inputs` and
+`outputs` sections of the tool file to find out what parameters are
+defined.
+
+```
+steps:
+ fastqc:
+ run: bio-cwl-tools/fastqc/fastqc_2.cwl
+ in:
+ reads_file: fq
+ out: [html_file, summary_file]
+```
+
+5. 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
+this with `{default: N}`
+
+
+```
+ STAR:
+ requirements:
+ ResourceRequirement:
+ ramMin: 6000
+ run: bio-cwl-tools/STAR/STAR-Align.cwl
+ in:
+ RunThreadN: {default: 4}
+ GenomeDir: genome
+ ForwardReads: fq
+ OutSAMtype: {default: BAM}
+ OutSAMunmapped: {default: Within}
+ out: [alignment]
+```
+
+6. Running samtools
+
+The third step is to generate an index for the aligned BAM.
+
+For this step, we need to use the output of a previous step as input
+to this step. We refer the output of a step by with name of the step
+(STAR), a slash, and the name of the output parameter (alignment), e.g. `STAR/alignment`
+
+This creates a dependency between steps. This means the `samtools`
+step will not run until the `STAR` step has completed successfully.
+
+```
+ samtools:
+ run: bio-cwl-tools/samtools/samtools_index.cwl
+ in:
+ bam_sorted: STAR/alignment
+ out: [bam_sorted_indexed]
+```
+
+7. featureCounts
+
+As of this writing, the `subread` package that provides
+`featureCounts` is not available in bio-cwl-tools (and if it has been
+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.
+
+8. Workflow Outputs
+
+The last thing to do is declare the workflow outputs in the `outputs` section.
+
+For each output, we need to declare the type of output, and what
+parameter has the output value.
+
+Output types are the same as input types, valid types include `File`,
+`Directory`, `string`, `boolean`, `int`, and `float`.
+
+The `outputSource` field refers the a step output in the same way that
+the `in` block does, the name of the step, a slash, and the name of
+the output parameter.
+
+For our final outputs, we want the results from fastqc and the
+aligned, sorted and indexed BAM file.
+
+```
+outputs:
+ qc_html:
+ type: File
+ outputSource: fastqc/html_file
+ qc_summary:
+ type: File
+ outputSource: fastqc/summary_file
+ bam_sorted_indexed:
+ type: File
+ outputSource: samtools/bam_sorted_indexed
+```
projects / rnaseq-cwl-training.git / blobdiff