2 title: "Turning a shell script into a workflow by composing existing tools"
6 - "Key question (FIXME)"
8 - "First learning objective. (FIXME)"
10 - "First key point. Brief Answer to questions. (FIXME)"
15 We will create a new git repository and import a library of existing
16 tool definitions that will help us build our workflow.
18 Create a new git repository to hold our workflow with this command:
21 git init rnaseq-cwl-training-exercises
27 git clone https://github.com/arvados/arvados-vscode-cwl-template.git rnaseq-cwl-training-exercises
30 Next, import bio-cwl-tools with this command:
33 git submodule add https://github.com/common-workflow-library/bio-cwl-tools.git
36 # Writing the workflow
40 Create a new file "main.cwl"
42 Start with this header.
48 label: RNAseq CWL practice workflow
53 The purpose of a workflow is to consume some input parameters, run a
54 series of steps, and produce output values.
56 For this analysis, the input parameters are the fastq file and the reference data required by STAR.
58 In the original shell script, the following variables are declared:
61 # initialize a variable with an intuitive name to store the name of the input fastq file
64 # directory with genome reference FASTA and index files + name of the gene annotation file
65 genome=rnaseq/reference_data
66 gtf=rnaseq/reference_data/chr1-hg19_genes.gtf
69 In CWL, we will declare these variables in the `inputs` section.
71 The inputs section lists each input parameter and its type. Valid
72 types include `File`, `Directory`, `string`, `boolean`, `int`, and
75 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:
86 A workflow consists of one or more steps. This is the `steps` section.
88 Now we need to describe the first step of the workflow. This step is to run `fastqc`.
90 A workflow step consists of the name of the step, the tool to `run`,
91 the input parameters to be passed to the tool in `in`, and the output
92 parameters expected from the tool in `out`.
94 The value of `run` references the tool file. Tip: while typing the
95 file name, you can get suggestions and auto-completion on a partial
96 name using control+space.
98 The `in` block lists input parameters to the tool and the workflow
99 parameters that will be assigned to those inputs.
101 The `out` block lists output parameters to the tool that are used
102 later in the workflow.
104 You need to know which input and output parameters are available for
105 each tool. In vscode, click on the value of `run` and select "Go to
106 definition" to open the tool file. Look for the `inputs` and
107 `outputs` sections of the tool file to find out what parameters are
113 run: bio-cwl-tools/fastqc/fastqc_2.cwl
119 ## 4. Running alignment with STAR
121 STAR has more parameters. Sometimes we want to provide input values
122 to a step without making them as workflow-level inputs. We can do
123 this with `{default: N}`
131 run: bio-cwl-tools/STAR/STAR-Align.cwl
133 RunThreadN: {default: 4}
136 OutSAMtype: {default: BAM}
137 OutSAMunmapped: {default: Within}
141 ## 5. Running samtools
143 The third step is to generate an index for the aligned BAM.
145 For this step, we need to use the output of a previous step as input
146 to this step. We refer the output of a step by with name of the step
147 (STAR), a slash, and the name of the output parameter (alignment), e.g. `STAR/alignment`
149 This creates a dependency between steps. This means the `samtools`
150 step will not run until the `STAR` step has completed successfully.
154 run: bio-cwl-tools/samtools/samtools_index.cwl
156 bam_sorted: STAR/alignment
157 out: [bam_sorted_indexed]
162 As of this writing, the `subread` package that provides
163 `featureCounts` is not available in bio-cwl-tools (and if it has been
164 added since writing this, let's pretend that it isn't there.) We will
165 go over how to write a CWL wrapper for a command line tool in
166 lesson 3. For now, we will leave off the final step.
168 ## 7. Workflow Outputs
170 The last thing to do is declare the workflow outputs in the `outputs` section.
172 For each output, we need to declare the type of output, and what
173 parameter has the output value.
175 Output types are the same as input types, valid types include `File`,
176 `Directory`, `string`, `boolean`, `int`, and `float`.
178 The `outputSource` field refers the a step output in the same way that
179 the `in` block does, the name of the step, a slash, and the name of
180 the output parameter.
182 For our final outputs, we want the results from fastqc and the
183 aligned, sorted and indexed BAM file.
189 outputSource: fastqc/html_file
192 outputSource: samtools/bam_sorted_indexed