- 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