- 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