Workflow: gdc workflow
Fetched 2021-03-03 21:02:43 GMT
Verified with cwltool version 1.0.20180525185854
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| reference | File |
Fasta file containing the reference corresponding to the bam files |
|
| transcriptome | File |
GTF file giving the transcriptome used to annotate against |
|
| tcga_sample | String |
String giving the TCGA sample id, i.e. TCGA-01-0001-01A |
|
| gdc_token | File |
gdc_token providing permission for downloading controlled access data |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| filter_vcf |
filter_vcf.cwl
(CommandLineTool)
|
||
| bgzip_vcf |
bgzip_vcf.cwl
(CommandLineTool)
|
||
| download_vcf |
download_vcf.cwl
(CommandLineTool)
|
||
| regtools |
../regtools/workflow.cwl
(Workflow)
|
regtools workflow | |
| obtain_manifest_vcf |
obtain_manifest_vcf.cwl
(CommandLineTool)
|
||
| download_bam |
download_bam.cwl
(CommandLineTool)
|
||
| merge_vcf |
merge_vcf.cwl
(CommandLineTool)
|
||
| decompress_vcf |
decompress_vcf.cwl
(CommandLineTool)
|
||
| obtain_manifest_bam |
obtain_manifest_bam.cwl
(CommandLineTool)
|
||
| index_vcf |
index_vcf.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| filtered_vcf_file | File |
Permalink:
https://w3id.org/cwl/view/git/c25ff825502cd51dbcf5aa72525ca9890cf8d70c/gdc_client/workflow.cwl
