Workflow: prefetch_fastq.cwl
Fetched 2024-05-18 21:44:59 GMT
Verified with cwltool version 3.1.20230201224320
Worfklow combining an SRA fetch from NCBI with a fastq-dump cmd
- 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 |
|---|---|---|---|
| sra_accession | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| prefetch |
prefetch.cwl
(CommandLineTool)
|
Tool runs prefetch from NCBI SRA toolkit |
|
| fastq_dump |
fastq_dump.cwl
(CommandLineTool)
|
Tool runs fastq-dump from NCBI SRA toolkit Supports only file inputs. Output file names are formed on the base of `sra_file` input basename. |
|
| rename_fastq1 |
../util/rename.cwl
(ExpressionTool)
|
Also consider https://www.commonwl.org/user_guide/misc/#rename-an-input-file or https://www.commonwl.org/user_guide/misc/#rename-an-output-file |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| fastq_files | File[] [FASTQ-illumina] | ||
| fastq_file_1 | File [FASTQ-illumina] | ||
| fastq_file_2 | File (Optional) [FASTQ-illumina] |
Permalink:
https://w3id.org/cwl/view/git/82b291f7d205024b2db7d4106a448c8a65855439/bio-cwl-tools/sratoolkit/prefetch_fastq.cwl
