Workflow: collapsed_fastq_to_bam.cwl
Fetched 2025-04-03 01:41:55 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 |
|---|---|---|---|
| fastq1 | File | ||
| fastq2 | File | ||
| add_rg_CN | String | ||
| add_rg_ID | String | ||
| add_rg_LB | Integer | ||
| add_rg_PL | String | ||
| add_rg_PU | String | ||
| add_rg_SM | String | ||
| run_tools | https://w3id.org/cwl/view/git/3441040dfaecba58150c13a95a6a93657b00778a/resources/schemas/collapsing_tools.yaml#run_tools | ||
| reference_fasta | String | ||
| reference_fasta_fai | String | ||
| add_or_replace_read_groups__params | https://w3id.org/cwl/view/git/3441040dfaecba58150c13a95a6a93657b00778a/resources/schemas/params/add_or_replace_read_groups.yaml#add_or_replace_read_groups__params |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| bwa_mem |
../../cwl_tools/bwa-mem/bwa-mem.cwl
(CommandLineTool)
|
||
| add_or_replace_read_groups |
../../cwl_tools/picard/AddOrReplaceReadGroups.cwl
(CommandLineTool)
|
None |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| bai | File | ||
| bam | File |
Permalink:
https://w3id.org/cwl/view/git/3441040dfaecba58150c13a95a6a93657b00778a/workflows/marianas/collapsed_fastq_to_bam.cwl
