Workflow: samples_fillout_workflow.cwl
Fetched 2025-08-16 00:59:27 GMT
Verified with cwltool version 3.1.20230201224320
Workflow to run GetBaseCountsMultiSample fillout on a number of samples, each with their own bam and maf 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/3bc4fab5503e58521ed0eb9c0d035ac18460dc13/cwl/types.yml#FilloutSample[] | ||
| ref_fasta | File | ||
| exac_filter | File | ||
| output_fname | String (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| gbcms |
57c09068ef251608f383e015cb250ec7
(CommandLineTool)
|
||
| maf2vcf |
3c76f7199b81c7d6a1d2293011d78a0f
(CommandLineTool)
|
||
| vcf_to_maf |
30d440f29c3a73bd63c8fe71ce56dd2b
(CommandLineTool)
|
||
| create_bam_list |
0cf9edb507da3a7470e007cda0613cb0
(ExpressionTool)
|
||
| split_filter_vcf |
de023759a89f02637ce1ceb2361dab7c
(CommandLineTool)
|
||
| create_samples_list |
4b62fe16e6a021301b87a2f7830bad09
(ExpressionTool)
|
||
| concat_with_comments |
bc35942b322fa664205bddfd65d847ed
(CommandLineTool)
|
||
| convert_to_portal_format |
update_cBioPortal_data.cwl
(CommandLineTool)
|
||
| fix_labels_and_merge_vcfs |
fd792dd654d1f5a7f012d3faf3c4d8fe
(CommandLineTool)
|
||
| create_fillout_targets_list |
c82438655f7fdf2ed3bb0dd424ecc45c
(CommandLineTool)
|
||
| create_clinical_samples_list |
20a83254237072344da564cf2ad87f97
(ExpressionTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| output_file | File | ||
| portal_file | File | ||
| filtered_file | File |
Permalink:
https://w3id.org/cwl/view/git/3bc4fab5503e58521ed0eb9c0d035ac18460dc13/cwl/samples_fillout_workflow.cwl
