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vcf_eval_cle_gold.cwl
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vcf_eval_cle_gold.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "CLE gold vcf evaluation workflow"
requirements:
- class: SubworkflowFeatureRequirement
- class: StepInputExpressionRequirement
inputs:
reference:
type:
- string
- File
secondaryFiles: [.fai, ^.dict]
roi_bed:
type: File
query_vcf:
type: File
secondaryFiles: [.tbi]
normal_cram:
type: File
secondaryFiles: [^.crai]
tumor_cram:
type: File
secondaryFiles: [^.crai]
normal_sample_name:
type: string?
default: 'NORMAL'
tumor_sample_name:
type: string?
default: 'TUMOR'
gold_vcf:
type: File
secondaryFiles: [.tbi]
true_negative_bed:
type: File
output_dir:
type: string
outputs:
output_directory:
type: Directory
outputSource: gather_to_sub_directory/gathered_directory
steps:
normal_cram_to_bam_and_index:
run: cram_to_bam_and_index.cwl
in:
cram: normal_cram
reference: reference
out:
[bam]
tumor_cram_to_bam_and_index:
run: cram_to_bam_and_index.cwl
in:
cram: tumor_cram
reference: reference
out:
[bam]
gold_vcf_roi:
run: ../tools/bedtools_intersect.cwl
in:
file_a: gold_vcf
file_b: roi_bed
output_file_a:
default: false
unique_result:
default: false
output_name:
default: 'gold_roi.vcf'
out:
[intersect_result]
bgzip_and_index_gold_roi:
run: bgzip_and_index.cwl
in:
vcf: gold_vcf_roi/intersect_result
out:
[indexed_vcf]
query_vcf_pass:
run: ../tools/select_variants.cwl
in:
reference: reference
vcf: query_vcf
exclude_filtered:
default: true
out:
[filtered_vcf]
query_vcf_pass_roi:
run: ../tools/bedtools_intersect.cwl
in:
file_a: query_vcf_pass/filtered_vcf
file_b: roi_bed
output_file_a:
default: false
unique_result:
default: false
output_name:
default: 'query_pass_roi.vcf'
out:
[intersect_result]
bgzip_and_index_query_pass_roi:
run: bgzip_and_index.cwl
in:
vcf: query_vcf_pass_roi/intersect_result
out:
[indexed_vcf]
combine_vcf:
run: ../tools/combine_variants_concordance.cwl
in:
reference: reference
base_vcf: bgzip_and_index_gold_roi/indexed_vcf
query_vcf: bgzip_and_index_query_pass_roi/indexed_vcf
out:
[combined_vcf]
normal_bam_readcount:
run: ../tools/bam_readcount.cwl
in:
vcf: combine_vcf/combined_vcf
sample: normal_sample_name
reference_fasta: reference
bam: normal_cram_to_bam_and_index/bam
out:
[snv_bam_readcount_tsv, indel_bam_readcount_tsv]
tumor_bam_readcount:
run: ../tools/bam_readcount.cwl
in:
vcf: combine_vcf/combined_vcf
sample: tumor_sample_name
reference_fasta: reference
bam: tumor_cram_to_bam_and_index/bam
out:
[snv_bam_readcount_tsv, indel_bam_readcount_tsv]
query_vcf_pass_snv:
run: ../tools/select_variants.cwl
in:
reference: reference
vcf: bgzip_and_index_query_pass_roi/indexed_vcf
select_type:
default: 'SNP'
out:
[filtered_vcf]
query_vcf_pass_indel:
run: ../tools/select_variants.cwl
in:
reference: reference
vcf: bgzip_and_index_query_pass_roi/indexed_vcf
select_type:
default: 'INDEL'
out:
[filtered_vcf]
true_negative_roi:
run: ../tools/bedtools_intersect.cwl
in:
file_a: true_negative_bed
file_b: roi_bed
output_file_a:
default: false
unique_result:
default: false
output_name:
default: 'tn_roi.bed'
out:
[intersect_result]
true_negative_intersect_query_snv:
run: ../tools/bedtools_intersect.cwl
in:
file_a: true_negative_roi/intersect_result
file_b: query_vcf_pass_snv/filtered_vcf
output_file_a:
default: false
unique_result:
default: false
output_name:
default: 'tn_x_query_snv.bed'
out:
[intersect_result]
true_negative_intersect_query_indel:
run: ../tools/bedtools_intersect.cwl
in:
file_a: true_negative_roi/intersect_result
file_b: query_vcf_pass_indel/filtered_vcf
output_file_a:
default: false
unique_result:
default: false
output_name:
default: 'tn_x_query_indel.bed'
out:
[intersect_result]
sompy:
run: ../tools/sompy.cwl
in:
reference: reference
roi_bed: roi_bed
truth_vcf: gold_vcf
query_vcf: query_vcf_pass/filtered_vcf
out:
[sompy_out]
evaluation:
run: ../tools/eval_cle_gold.cwl
in:
sompy_out: sompy/sompy_out
true_negative_bed: true_negative_roi/intersect_result
tn_x_query_snv: true_negative_intersect_query_snv/intersect_result
tn_x_query_indel: true_negative_intersect_query_indel/intersect_result
combined_vcf: combine_vcf/combined_vcf
normal_snv_bam_readcount_tsv: normal_bam_readcount/snv_bam_readcount_tsv
normal_indel_bam_readcount_tsv: normal_bam_readcount/indel_bam_readcount_tsv
tumor_snv_bam_readcount_tsv: tumor_bam_readcount/snv_bam_readcount_tsv
tumor_indel_bam_readcount_tsv: tumor_bam_readcount/indel_bam_readcount_tsv
out:
[eval_out, vaf_report]
gather_to_sub_directory:
run: ../tools/gather_to_sub_directory.cwl
in:
outdir: output_dir
files: [evaluation/eval_out,evaluation/vaf_report]
out:
[gathered_directory]