Workflow: alignment workflow
Fetched 2025-08-19 15:37:44 GMT
Verified with cwltool version 3.1.20230201224320
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
MIT License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| bam | File |
bam file to align |
|
| reference | File |
gzipped reference fasta to align to |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| sam2bam |
sam2bam.cwl
(CommandLineTool)
|
||
| sort_bam |
sort_bam.cwl
(CommandLineTool)
|
||
| bwa_index |
bwa_index.cwl
(CommandLineTool)
|
||
| gnu_unzip |
gunzip.cwl
(CommandLineTool)
|
||
| index_bam |
bam_index.cwl
(CommandLineTool)
|
||
| index_ref |
index_fa.cwl
(CommandLineTool)
|
||
| sam2fastq |
sam2fastq.cwl
(CommandLineTool)
|
||
| align_fastq |
bwa_mem.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| bam_index_out | File | ||
| index_ref_out | File |
Permalink:
https://w3id.org/cwl/view/git/b6891cd125b50b1d7cb9043f808fb67cfdd6b836/assets/CWL/workflow.cwl
