Workflow: test-workflow
Fetched 2021-01-14 05:08:09 GMT
Verified with cwltool version 1.0.20180525185854
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
https://raw.githubusercontent.com/pjotrp/CWL-workflows/30fe60ed62d64e45ac2de30117096e8697d08475/LICENSE
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| fq1 | File [FASTQ] |
FastQ file from next-generation sequencers |
|
| fq2 | File [FASTQ] |
FastQ file from next-generation sequencers |
|
| ref | File [FASTA] |
reference (e.g., hs37d5) in fasta format |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| map |
../Tools/bwa-mem-PE.cwl
(CommandLineTool)
|
bwa-mem-PE-0.7.4--ha92aebf_0 | |
| qc1 |
../Tools/fastqc.cwl
(CommandLineTool)
|
fastqc | |
| qc2 |
../Tools/fastqc.cwl
(CommandLineTool)
|
fastqc | |
| qc1P |
../Tools/fastqc.cwl
(CommandLineTool)
|
fastqc | |
| qc2P |
../Tools/fastqc.cwl
(CommandLineTool)
|
fastqc | |
| trimPE |
../Tools/trimmomaticPE.cwl
(CommandLineTool)
|
trimmomatic-0.38 |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| sam | File | ||
| oqc1 | File | ||
| oqc2 | File | ||
| oqc1P | File | ||
| oqc2P | File |
Permalink:
https://w3id.org/cwl/view/git/30fe60ed62d64e45ac2de30117096e8697d08475/Workflows/test-workflow.cwl
