Workflow: samples_fillout_index_batch_workflow.cwl
Fetched 2026-01-05 05:57:24 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
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- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| is_impact | Boolean | ||
| ref_fasta | File | ||
| exac_filter | File | ||
| sample_groups | 386d151e2d0c47c35be4ada99e67fcd2[] |
a nested list of lists of grouped samples |
|
| argos_version_string | String (Optional) | ||
| fillout_output_fname | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| concat_singletons |
4f9b238f8915b8ced9644d103f71d292
(CommandLineTool)
|
||
| concat_portal_file |
concat-tables.cwl
(CommandLineTool)
|
||
| concat_output_files |
concat-tables.cwl
(CommandLineTool)
|
||
| concat_filtered_file |
concat-tables.cwl
(CommandLineTool)
|
||
| concat_uncalled_file |
concat-tables.cwl
(CommandLineTool)
|
||
| split_singleton_groups |
45a087753b78eb17d35977fbd09530a9
(ExpressionTool)
|
||
| run_samples_fillout_index_workflow |
samples_fillout_index_workflow.cwl
(Workflow)
|
Wrapper to run bam indexing on all bams before submitting for samples fillout Also includes steps to pre-filter some maf input files |
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_batch_workflow.cwl
