Workflow: regtools workflow
Fetched 2025-12-21 14:20:01 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 |
|---|---|---|---|
| e | String[] (Optional) | ||
| i | String[] (Optional) | ||
| variants | File |
VCF file providing somatic variant calls |
|
| reference | File |
Fasta file containing the reference corresponding to the bam files |
|
| rna_tumor_bam | File |
RNAseq aligned tumor bam |
|
| transcriptome | File |
GTF file giving the transcriptome used to annotate against |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| junctions_extract |
junctions_extract.cwl
(CommandLineTool)
|
||
| cis_splice_effects |
cis_splice_effects.cwl
(CommandLineTool)
|
||
| junctions_annotate |
junctions_annotate.cwl
(CommandLineTool)
|
||
| cis_splice_effects_v2 |
cis_splice_effects_v2.cwl
(CommandLineTool)
|
||
| cis_splice_effects_v3 |
cis_splice_effects_v3.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| junctions_extract_out | File | ||
| junctions_annotate_out | File | ||
| cis_splice_effects_identify | File[] | ||
| cis_splice_effects_identify_v2 | File | ||
| cis_splice_effects_identify_v3 | File |
Permalink:
https://w3id.org/cwl/view/git/c25ff825502cd51dbcf5aa72525ca9890cf8d70c/regtools/workflow.cwl
