- 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 |
---|---|---|---|
roi_bed | File | ||
gold_vcf | File | ||
query_vcf | File | ||
reference | File | ||
output_dir | String | ||
tumor_cram | File | ||
normal_cram | File | ||
true_negative_bed | File | ||
tumor_sample_name | String (Optional) | ||
normal_sample_name | String (Optional) |
Steps
ID | Runs | Label | Doc |
---|---|---|---|
sompy |
../tools/sompy.cwl
(CommandLineTool)
|
som.py compares variants in vcf by location and alleles (using bcftools isec). | |
evaluation |
../tools/eval_cle_gold.cwl
(CommandLineTool)
|
Make CLE gold evaluation output and vaf report | |
combine_vcf |
../tools/combine_variants_concordance.cwl
(CommandLineTool)
|
CombineVariants (GATK 3.6) | |
gold_vcf_roi |
../tools/bedtools_intersect.cwl
(CommandLineTool)
|
||
query_vcf_pass |
../tools/select_variants.cwl
(CommandLineTool)
|
SelectVariants (GATK 4.1.8.1) | |
true_negative_roi |
../tools/bedtools_intersect.cwl
(CommandLineTool)
|
||
query_vcf_pass_roi |
../tools/bedtools_intersect.cwl
(CommandLineTool)
|
||
query_vcf_pass_snv |
../tools/select_variants.cwl
(CommandLineTool)
|
SelectVariants (GATK 4.1.8.1) | |
tumor_bam_readcount |
../tools/bam_readcount.cwl
(CommandLineTool)
|
run bam-readcount | |
normal_bam_readcount |
../tools/bam_readcount.cwl
(CommandLineTool)
|
run bam-readcount | |
query_vcf_pass_indel |
../tools/select_variants.cwl
(CommandLineTool)
|
SelectVariants (GATK 4.1.8.1) | |
gather_to_sub_directory |
../tools/gather_to_sub_directory.cwl
(CommandLineTool)
|
||
bgzip_and_index_gold_roi |
bgzip_and_index.cwl
(Workflow)
|
bgzip and index VCF | |
tumor_cram_to_bam_and_index |
cram_to_bam_and_index.cwl
(Workflow)
|
cram_to_bam workflow | |
normal_cram_to_bam_and_index |
cram_to_bam_and_index.cwl
(Workflow)
|
cram_to_bam workflow | |
bgzip_and_index_query_pass_roi |
bgzip_and_index.cwl
(Workflow)
|
bgzip and index VCF | |
true_negative_intersect_query_snv |
../tools/bedtools_intersect.cwl
(CommandLineTool)
|
||
true_negative_intersect_query_indel |
../tools/bedtools_intersect.cwl
(CommandLineTool)
|
Outputs
ID | Type | Label | Doc |
---|---|---|---|
output_directory | Directory |
Permalink:
https://w3id.org/cwl/view/git/a08de598edc04f340fdbff76c9a92336a7702022/definitions/subworkflows/vcf_eval_cle_gold.cwl