- 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 |
---|---|---|---|
bams | File[] | ||
run_tools | https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/resources/schemas/collapsing_tools.yaml#run_tools | ||
patient_id | String | ||
abra__params | https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/resources/schemas/params/abra.yaml#abra__params | ||
reference_fasta | String | ||
print_reads__params | https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/resources/schemas/params/print_reads.yaml#print_reads__params | ||
bqsr__knownSites_dbSNP | File | ||
bqsr__knownSites_millis | File | ||
base_recalibrator__params | https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/resources/schemas/params/base_recalibrator.yaml#base_recalibrator__params | ||
fix_mate_information__params | https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/resources/schemas/params/fix_mate_information.yaml#fix_mate_information__params | ||
find_covered_intervals__params | https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/resources/schemas/params/find_covered_intervals.yaml#find_covered_intervals__params |
Steps
ID | Runs | Label | Doc |
---|---|---|---|
ABRA_workflow |
ABRA/abra_workflow.cwl
(Workflow)
|
||
BQSR_workflow |
BQSR/bqsr_workflow.cwl
(Workflow)
|
Outputs
ID | Type | Label | Doc |
---|---|---|---|
covint_bed | File | ||
covint_list | File | ||
standard_bams | File[] | ||
recalibrated_scores_matrix | File[] |
Permalink:
https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/workflows/module-2.cwl