Workflow: gatk-4.0.0.0-library-cram-to-gvcfs.cwl
Fetched 2023-01-15 00:47:43 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| chunks | Integer | ||
| pcr_free | Boolean | ||
| library_cram | File | ||
| intersect_file | File | ||
| ref_fasta_files | File[] | ||
| haploid_chromosome_regex | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| cap_crams |
capmq.cwl
(Workflow)
|
||
| cram_get_fasta |
cram-get-fasta.cwl
(Workflow)
|
||
| haplotype_caller_diploid |
gatk-4.0.0.0-haplotypecaller.cwl
(Workflow)
|
||
| haplotype_caller_haploid |
gatk-4.0.0.0-haplotypecaller.cwl
(Workflow)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| reference | File | ||
| intervals_diploid | File[] | ||
| intervals_haploid | File[] | ||
| gvcf_files_diploid | File[] | ||
| gvcf_files_haploid | File[] |
Permalink:
https://w3id.org/cwl/view/git/8d9c9155a49045762cbf5a1e584fc20517b8be87/cwl/workflows/gatk-4.0.0.0-library-cram-to-gvcfs.cwl
