# Running and debugging a workflow
-1. The input parameter file
+### 1. The input parameter file
CWL input values are provided in the form of a YAML or JSON file.
Create one by right clicking on the explorer, select "New File" and
`class: File` or `class: Directory`. This distinguishes them from
plain strings that may or may not be file paths.
-
-## Arvados
+Note: if you don't have example sequence data or the STAR index files, see the Appendix below.
```
fq:
class: File
- location: keep:9178fe1b80a08a422dbe02adfd439764+925/raw_fastq/Mov10_oe_1.subset.fq
+ location: rnaseq/raw_fastq/Mov10_oe_1.subset.fq
format: http://edamontology.org/format_1930
genome:
class: Directory
- location: keep:02a12ce9e2707610991bd29d38796b57+2912
+ location: hg19-chr1-STAR-index
gtf:
class: File
- location: keep:9178fe1b80a08a422dbe02adfd439764+925/reference_data/chr1-hg19_genes.gtf
+ location: rnaseq/reference_data/chr1-hg19_genes.gtf
```
-## Generic
-
-Note: if you don't have example sequence data or the STAR index files, see the Appendix below.
+On Arvados, do this:
```
fq:
class: File
- location: rnaseq/raw_fastq/Mov10_oe_1.subset.fq
+ location: keep:9178fe1b80a08a422dbe02adfd439764+925/raw_fastq/Mov10_oe_1.subset.fq
format: http://edamontology.org/format_1930
genome:
class: Directory
- location: hg19-chr1-STAR-index
+ location: keep:02a12ce9e2707610991bd29d38796b57+2912
gtf:
class: File
- location: rnaseq/reference_data/chr1-hg19_genes.gtf
+ location: keep:9178fe1b80a08a422dbe02adfd439764+925/reference_data/chr1-hg19_genes.gtf
```
-2. Running the workflow
-
-## Arvados
-
-In vscode, select "main.cwl" and then choose "Terminal -> Run task -> Run CWL workflow on Arvados"
-
-## Generic
+### 2. Running the workflow
Type this into the terminal:
cwl-runner main.cwl main-input.yaml
```
-3. Debugging the workflow
+On Arvados with vscode, select "main.cwl" and then choose "Terminal -> Run task -> Run CWL workflow on Arvados"
+
+### 3. Debugging the workflow
A workflow can fail for many reasons: some possible reasons include
bad input, bugs in the code, or running out memory. In this case, the
If this happens, you will need to request more RAM.
-4. Setting runtime RAM requirements
+### 4. Setting runtime RAM requirements
By default, a step is allocated 256 MB of RAM. From the STAR error message:
After setting the RAM requirements, re-run the workflow.
-5. Workflow results
+### 5. Workflow results
The CWL runner will print a results JSON object to standard output. It will look something like this (it may include additional fields).