- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
MIT License
Note that the tools invoked by the workflow may have separate licenses.
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 | ||
scatter_count | Integer | ||
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 | |
merge_snvs |
../tools/set_filter_status.cwl
(CommandLineTool)
|
create filtered VCF | |
merge_indels |
../tools/set_filter_status.cwl
(CommandLineTool)
|
create filtered VCF | |
intervals_to_bed |
../tools/intervals_to_bed.cwl
(CommandLineTool)
|
||
index_merged_snvs |
../tools/index_vcf.cwl
(CommandLineTool)
|
vcf index | |
index_merged_indels |
../tools/index_vcf.cwl
(CommandLineTool)
|
vcf index | |
rename_tumor_sample |
../tools/replace_vcf_sample_name.cwl
(CommandLineTool)
|
||
split_interval_list |
../tools/split_interval_list.cwl
(CommandLineTool)
|
||
rename_normal_sample |
../tools/replace_vcf_sample_name.cwl
(CommandLineTool)
|
||
merge_scattered_somatic_snvs |
../tools/picard_merge_vcfs.cwl
(CommandLineTool)
|
Picard MergeVcfs | |
merge_scattered_somatic_indels |
../tools/picard_merge_vcfs.cwl
(CommandLineTool)
|
Picard MergeVcfs | |
merge_scattered_somatic_hc_snvs |
../tools/picard_merge_vcfs.cwl
(CommandLineTool)
|
Picard MergeVcfs | |
merge_scattered_somatic_hc_indels |
../tools/picard_merge_vcfs.cwl
(CommandLineTool)
|
Picard MergeVcfs |
Outputs
ID | Type | Label | Doc |
---|---|---|---|
filtered_vcf | File | ||
unfiltered_vcf | File |
Permalink:
https://w3id.org/cwl/view/git/9cbf2a483e1b9e4cdb8e2564be27a9e64fc1169e/definitions/subworkflows/varscan_pre_and_post_processing.cwl