Workflow: samples_fillout_index_workflow.cwl
Fetched 2024-12-26 04:18:35 GMT
Verified with cwltool version 3.1.20230201224320
Wrapper to run indexing on all bams before submitting for samples fillout Includes secondary input channels to allow for including .bam files that do not have indexes Also include other extra handling needed for files that might not meet needs for the fillout workflow NOTE: need v1.1 upgrade so we can do it all from a single channel with optional secondary files; https://www.commonwl.org/v1.1/CommandLineTool.html#SecondaryFileSchema
- Selected
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- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| samples | d4fae7ed528615322d6e31657754caad[] | ||
| bam_files | File[] | ||
| is_impact | Boolean | ||
| ref_fasta | File | ||
| exac_filter | File | ||
| unindexed_samples | 9f76e477d79942f5013e6b363b5ac232[] | ||
| unindexed_bam_files | File[] | ||
| argos_version_string | String (Optional) | ||
| fillout_output_fname | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| run_indexer |
index_bam.cwl
(CommandLineTool)
|
cmo-index | |
| run_maf_filter |
maf_filter.cwl
(CommandLineTool)
|
||
| run_samples_fillout |
samples_fillout_workflow.cwl
(Workflow)
|
Workflow to run GetBaseCountsMultiSample fillout on a number of samples, each with their own bam and maf files |
|
| run_maf_filter_unindexed |
maf_filter.cwl
(CommandLineTool)
|
||
| merge_samples_replace_mafs |
samples_fillout_index_workflow.cwl#merge_samples_replace_mafs/b358afc5-fb0e-49fd-9bc1-879a02a2e2a6
(ExpressionTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| output_file | File |
Permalink:
https://w3id.org/cwl/view/git/342e6f1f4f7a3839e579fbe96ccc8d6f7a61ac77/cwl/samples_fillout_index_workflow.cwl
