Workflow: samples_fillout_index_workflow.cwl
Fetched 2025-08-23 19:42:33 GMT
Verified with cwltool version 3.1.20230201224320
Wrapper to run bam indexing on all bams before submitting for samples fillout Also includes steps to pre-filter some maf input files
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| samples | https://w3id.org/cwl/view/git/2e1a01a788126f2901ffecc92a48fcbcb81776e1/cwl/types.yml#FilloutIndexSample[] | ||
| is_impact | Boolean | ||
| ref_fasta | File | ||
| exac_filter | File | ||
| argos_version_string | String (Optional) | ||
| fillout_output_fname | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| index_bam |
8f265671f58d118c50fdc47c77ae9b91
(CommandLineTool)
|
||
| prefilter_workflow |
b20eadce6ca442cc0c00e34fa168d62f
(Workflow)
|
||
| split_sample_groups |
5072b115aa2fa03e0ee031dead5191cb
(ExpressionTool)
|
||
| convert_sample_types |
80a367f647a34d3d49fc620f1b6e002e
(ExpressionTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| output_file | File | ||
| portal_file | File | ||
| filtered_file | File | ||
| uncalled_file | File |
Permalink:
https://w3id.org/cwl/view/git/2e1a01a788126f2901ffecc92a48fcbcb81776e1/cwl/samples_fillout_index_workflow.cwl
