- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
ID | Type | Title | Doc |
---|---|---|---|
p_value | Float (Optional) | ||
reference | File | ||
tumor_bam | File | ||
normal_bam | File | ||
min_coverage | Integer (Optional) | ||
min_var_freq | Float (Optional) | ||
interval_list | File | ||
strand_filter | Integer (Optional) | ||
max_normal_freq | Float (Optional) | ||
tumor_sample_name | String | ||
normal_sample_name | String |
Steps
ID | Runs | Label | Doc |
---|---|---|---|
index |
../tools/index_vcf.cwl
(CommandLineTool)
|
vcf index | |
merge |
../tools/merge_vcf.cwl
(CommandLineTool)
|
vcf merge | |
filter |
fp_filter.cwl
(Workflow)
|
fp_filter workflow | |
varscan |
varscan.cwl
(Workflow)
|
varscan somatic workflow | |
index_snvs |
../tools/index_vcf.cwl
(CommandLineTool)
|
vcf index | |
merge_snvs |
../tools/set_filter_status.cwl
(CommandLineTool)
|
create filtered VCF | |
index_indels |
../tools/index_vcf.cwl
(CommandLineTool)
|
vcf index | |
merge_indels |
../tools/set_filter_status.cwl
(CommandLineTool)
|
create filtered VCF | |
intervals_to_bed |
../tools/intervals_to_bed.cwl
(CommandLineTool)
|
||
rename_tumor_sample |
../tools/replace_vcf_sample_name.cwl
(CommandLineTool)
|
||
bgzip_and_index_snvs |
bgzip_and_index.cwl
(Workflow)
|
bgzip and index VCF | |
rename_normal_sample |
../tools/replace_vcf_sample_name.cwl
(CommandLineTool)
|
||
bgzip_and_index_indels |
bgzip_and_index.cwl
(Workflow)
|
bgzip and index VCF | |
bgzip_and_index_hc_snvs |
bgzip_and_index.cwl
(Workflow)
|
bgzip and index VCF | |
bgzip_and_index_hc_indels |
bgzip_and_index.cwl
(Workflow)
|
bgzip and index VCF |
Outputs
ID | Type | Label | Doc |
---|---|---|---|
filtered_vcf | File | ||
unfiltered_vcf | File |
Permalink:
https://w3id.org/cwl/view/git/336f7d1af649f42543baa6be2594cd872919b5b5/definitions/subworkflows/varscan_pre_and_post_processing.cwl