2 title: "Make a workflow by composing tools"
6 - "Key question (FIXME)"
8 - "First learning objective. (FIXME)"
10 - "First key point. Brief Answer to questions. (FIXME)"
15 Create a new file "main.cwl"
17 Start with this header.
23 label: RNAseq CWL practice workflow
28 The purpose of a workflow is to consume some input parameters, run a
29 series of steps, and produce output values.
31 For this analysis, the input parameters are the fastq file and the reference data required by STAR.
33 In the original shell script, the following variables are declared:
36 # initialize a variable with an intuitive name to store the name of the input fastq file
39 # directory with genome reference FASTA and index files + name of the gene annotation file
40 genome=rnaseq/reference_data
41 gtf=rnaseq/reference_data/chr1-hg19_genes.gtf
44 In CWL, we will declare these variables in the `inputs` section.
46 The inputs section lists each input parameter and its type. Valid
47 types include `File`, `Directory`, `string`, `boolean`, `int`, and
50 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:
61 A workflow consists of one or more steps. This is the `steps` section.
63 Now we need to describe the first step of the workflow. This step is to run `fastqc`.
65 A workflow step consists of the name of the step, the tool to `run`,
66 the input parameters to be passed to the tool in `in`, and the output
67 parameters expected from the tool in `out`.
69 The value of `run` references the tool file. Tip: while typing the
70 file name, you can get suggestions and auto-completion on a partial
71 name using control+space.
73 The `in` block lists input parameters to the tool and the workflow
74 parameters that will be assigned to those inputs.
76 The `out` block lists output parameters to the tool that are used
77 later in the workflow.
79 You need to know which input and output parameters are available for
80 each tool. In vscode, click on the value of `run` and select "Go to
81 definition" to open the tool file. Look for the `inputs` and
82 `outputs` sections of the tool file to find out what parameters are
88 run: bio-cwl-tools/fastqc/fastqc_2.cwl
94 # 4. Running alignment with STAR
96 STAR has more parameters. Sometimes we want to provide input values
97 to a step without making them as workflow-level inputs. We can do
98 this with `{default: N}`
106 run: bio-cwl-tools/STAR/STAR-Align.cwl
108 RunThreadN: {default: 4}
111 OutSAMtype: {default: BAM}
112 OutSAMunmapped: {default: Within}
116 # 5. Running samtools
118 The third step is to generate an index for the aligned BAM.
120 For this step, we need to use the output of a previous step as input
121 to this step. We refer the output of a step by with name of the step
122 (STAR), a slash, and the name of the output parameter (alignment), e.g. `STAR/alignment`
124 This creates a dependency between steps. This means the `samtools`
125 step will not run until the `STAR` step has completed successfully.
129 run: bio-cwl-tools/samtools/samtools_index.cwl
131 bam_sorted: STAR/alignment
132 out: [bam_sorted_indexed]
137 As of this writing, the `subread` package that provides
138 `featureCounts` is not available in bio-cwl-tools (and if it has been
139 added since writing this, let's pretend that it isn't there.) We will
140 go over how to write a CWL wrapper for a command line tool in
141 lesson 3. For now, we will leave off the final step.
143 # 7. Workflow Outputs
145 The last thing to do is declare the workflow outputs in the `outputs` section.
147 For each output, we need to declare the type of output, and what
148 parameter has the output value.
150 Output types are the same as input types, valid types include `File`,
151 `Directory`, `string`, `boolean`, `int`, and `float`.
153 The `outputSource` field refers the a step output in the same way that
154 the `in` block does, the name of the step, a slash, and the name of
155 the output parameter.
157 For our final outputs, we want the results from fastqc and the
158 aligned, sorted and indexed BAM file.
164 outputSource: fastqc/html_file
167 outputSource: samtools/bam_sorted_indexed