Workflow: collapsed_fastq_to_bam.cwl
Fetched 2023-04-01 05:10:09 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 | ||
| tmp_dir | String | ||
| 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 | |||
| output_suffix | String | ||
| reference_fasta | String | ||
| reference_fasta_fai | String |
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/9998da2da694af2edad7c2135f6995e2282794a3/workflows/marianas/collapsed_fastq_to_bam.cwl
