WGS Germline (Multi callers) [VARIANTS only]¶
WGSGermlineMultiCallersVariantsOnly
· A variant-calling WGS pipeline using GATK, VarDict and Strelka2 · 3 contributors · 1 version
This workflow is a reference pipeline using the Janis Python framework (pipelines assistant).
- Call the appropriate variant callers (GRIDSS / GATK / Strelka / VarDict);
- Merges the variants from GATK / Strelka / VarDict.
- Outputs the final variants in the VCF format.
Resources
This pipeline has been tested using the HG38 reference set, available on Google Cloud Storage through:
This pipeline expects the assembly references to be as they appear in that storage (“.fai”, “.amb”, “.ann”, “.bwt”, “.pac”, “.sa”, “^.dict”). The known sites (snps_dbsnp, snps_1000gp, known_indels, mills_indels) should be gzipped and tabix indexed.
Quickstart¶
- Install Janis
- Ensure Janis is configured to work with Docker or Singularity.
- Ensure all reference files are available:
Note
More information about these inputs are available below.
Name | Type | Source | Description |
---|---|---|---|
reference | FastaWithIndexes |
|
The reference genome from which to align the reads. This requires a number indexes (can be generated with the ‘IndexFasta’ pipeline This pipeline has been tested using the HG38 reference set.
|
snps_dbsnp | Gzipped<VCF> |
|
From the GATK resource bundle, passed to BaseRecalibrator as known_sites |
snps_1000gp | Gzipped<VCF> |
|
From the GATK resource bundle, passed to BaseRecalibrator as known_sites . Accessible from the HG38 genomics-public-data google cloud bucket: https://console.cloud.google.com/storage/browser/genomics-public-data/references/hg38/v0/ |
known_indels | Gzipped<VCF> |
|
From the GATK resource bundle, passed to BaseRecalibrator as known_sites |
mills_indels | Gzipped<VCF> |
|
From the GATK resource bundle, passed to BaseRecalibrator as known_sites |
gridss_blacklist | bed | BED file containing regions to ignore. For more information, visit: https://github.com/PapenfussLab/gridss#blacklist | |
gatk_intervals | Array<bed> | None | List of intervals over which to split the GATK variant calling |
vardict_intervals | Array<bed> | None | List of intervals over which to split the VarDict variant calling |
strelka_intervals | Gzipped<bed> | None | An interval for which to restrict the analysis to. |
- Generate user and static input files for WGSGermlineMultiCallersVariantsOnly:
# user inputs
janis inputs --user WGSGermlineMultiCallersVariantsOnly > inputs.yaml
# static inputs
janis inputs --static WGSGermlineMultiCallersVariantsOnly > static.yaml
inputs.yaml
bam: NA12878.bam
sample_name: NA12878
static.yaml
gatk_intervals: BRCA1.bed
gridss_blacklist: gridss_blacklist.bed
known_indels: Homo_sapiens_assembly38.known_indels.vcf.gz
mills_indels: Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
reference: Homo_sapiens_assembly38.fasta
snps_1000gp: 1000G_phase1.snps.high_confidence.hg38.vcf.gz
snps_dbsnp: Homo_sapiens_assembly38.dbsnp138.vcf.gz
strelka_intervals: BRCA1.bed.gz
vardict_intervals: BRCA1.bed
- Run WGSGermlineMultiCallersVariantsOnly with:
janis run [...run options] \
--inputs inputs.yaml \
--inputs static.yaml \
WGSGermlineMultiCallersVariantsOnly
Outputs¶
name | type | documentation |
---|---|---|
out_performance_summary | csv | A text file of performance summary of bam |
out_gridss_assembly | BAM | Assembly returned by GRIDSS |
out_variants_gridss | VCF | Variants from the GRIDSS variant caller |
out_variants_gatk | Gzipped<VCF> | Merged variants from the GATK caller |
out_variants_gatk_split | Array<VCF> | Unmerged variants from the GATK caller (by interval) |
out_variants_strelka | VCF | Variants from the Strelka variant caller |
out_variants_vardict | Gzipped<VCF> | Merged variants from the VarDict caller |
out_variants_vardict_split | Array<VCF> | Unmerged variants from the VarDict caller (by interval) |
out_variants | VCF | Combined variants from all 3 callers |
Workflow¶
Information¶
ID: | WGSGermlineMultiCallersVariantsOnly |
---|---|
Versions: | 1.4.0 |
Authors: | Michael Franklin, Richard Lupat, Jiaan Yu |
Citations: | |
Created: | None |
Updated: | None |
Embedded Tools¶
Generate genome for BedtoolsCoverage | GenerateGenomeFileForBedtoolsCoverage/v0.1.0 |
Performance summary workflow (whole genome) | PerformanceSummaryGenome/v0.1.0 |
Gridss | gridss/v2.6.2 |
GATK Base Recalibration on Bam | GATKBaseRecalBQSRWorkflow/4.1.3 |
GATK4 Germline Variant Caller | GATK4_GermlineVariantCaller/4.1.3.0 |
GATK4: Gather VCFs | Gatk4GatherVcfs/4.1.3.0 |
BGZip | bgzip/1.2.1 |
BCFTools: Sort | bcftoolssort/v1.9 |
UncompressArchive | UncompressArchive/v1.0.0 |
Strelka Germline Variant Caller | strelkaGermlineVariantCaller/v0.1.1 |
GenerateVardictHeaderLines | GenerateVardictHeaderLines/v0.1.0 |
Vardict Germline Variant Caller | vardictGermlineVariantCaller/v0.1.1 |
Combine Variants | combinevariants/0.0.8 |
Annotate Bam Stats to Germline Vcf Workflow | AddBamStatsGermline/v0.1.0 |
Additional configuration (inputs)¶
name | type | documentation |
---|---|---|
sample_name | String | Sample name from which to generate the readGroupHeaderLine for BwaMem |
bam | IndexedBam | Input indexed bam (+ .bam.bai) to process. You only specify the primary sample.bam, and the index (eg: NA12878.bam.bai) will be picked up automatically. |
reference | FastaWithIndexes | The reference genome from which to align the reads. This requires a number indexes (can be generated with the ‘IndexFasta’ pipeline This pipeline has been tested using the HG38 reference set.
|
snps_dbsnp | Gzipped<VCF> | From the GATK resource bundle, passed to BaseRecalibrator as known_sites |
snps_1000gp | Gzipped<VCF> | From the GATK resource bundle, passed to BaseRecalibrator as known_sites . Accessible from the HG38 genomics-public-data google cloud bucket: https://console.cloud.google.com/storage/browser/genomics-public-data/references/hg38/v0/ |
known_indels | Gzipped<VCF> | From the GATK resource bundle, passed to BaseRecalibrator as known_sites |
mills_indels | Gzipped<VCF> | From the GATK resource bundle, passed to BaseRecalibrator as known_sites |
gridss_blacklist | bed | BED file containing regions to ignore. For more information, visit: https://github.com/PapenfussLab/gridss#blacklist |
gatk_intervals | Array<bed> | List of intervals over which to split the GATK variant calling |
vardict_intervals | Array<bed> | List of intervals over which to split the VarDict variant calling |
strelka_intervals | Gzipped<bed> | An interval for which to restrict the analysis to. |
vc_vardict_allele_freq_threshold | Optional<Float> | |
combine_variants_type | Optional<String> | germline | somatic |
combine_variants_columns | Optional<Array<String>> | Columns to keep, seperated by space output vcf (unsorted) |
Workflow Description Language¶
version development
import "tools/GenerateGenomeFileForBedtoolsCoverage_v0_1_0.wdl" as G
import "tools/PerformanceSummaryGenome_v0_1_0.wdl" as P
import "tools/gridss_v2_6_2.wdl" as G2
import "tools/GATKBaseRecalBQSRWorkflow_4_1_3.wdl" as G3
import "tools/GATK4_GermlineVariantCaller_4_1_3_0.wdl" as G4
import "tools/Gatk4GatherVcfs_4_1_3_0.wdl" as G5
import "tools/bgzip_1_2_1.wdl" as B
import "tools/bcftoolssort_v1_9.wdl" as B2
import "tools/UncompressArchive_v1_0_0.wdl" as U
import "tools/strelkaGermlineVariantCaller_v0_1_1.wdl" as S
import "tools/GenerateVardictHeaderLines_v0_1_0.wdl" as G6
import "tools/vardictGermlineVariantCaller_v0_1_1.wdl" as V
import "tools/combinevariants_0_0_8.wdl" as C
import "tools/AddBamStatsGermline_v0_1_0.wdl" as A
workflow WGSGermlineMultiCallersVariantsOnly {
input {
String sample_name
File bam
File bam_bai
File reference
File reference_fai
File reference_amb
File reference_ann
File reference_bwt
File reference_pac
File reference_sa
File reference_dict
File snps_dbsnp
File snps_dbsnp_tbi
File snps_1000gp
File snps_1000gp_tbi
File known_indels
File known_indels_tbi
File mills_indels
File mills_indels_tbi
File gridss_blacklist
Array[File] gatk_intervals
Array[File] vardict_intervals
File strelka_intervals
File strelka_intervals_tbi
Float? vc_vardict_allele_freq_threshold = 0.05
String? combine_variants_type = "germline"
Array[String]? combine_variants_columns = ["AC", "AN", "AF", "AD", "DP", "GT"]
}
call G.GenerateGenomeFileForBedtoolsCoverage as calculate_performancesummary_genomefile {
input:
reference=reference,
reference_dict=reference_dict
}
call P.PerformanceSummaryGenome as performance_summary {
input:
bam=bam,
bam_bai=bam_bai,
sample_name=sample_name,
genome_file=calculate_performancesummary_genomefile.out
}
call G2.gridss as vc_gridss {
input:
bams=[bam],
bams_bai=[bam_bai],
reference=reference,
reference_fai=reference_fai,
reference_amb=reference_amb,
reference_ann=reference_ann,
reference_bwt=reference_bwt,
reference_pac=reference_pac,
reference_sa=reference_sa,
reference_dict=reference_dict,
blacklist=gridss_blacklist
}
scatter (g in gatk_intervals) {
call G3.GATKBaseRecalBQSRWorkflow as bqsr {
input:
bam=bam,
bam_bai=bam_bai,
intervals=g,
reference=reference,
reference_fai=reference_fai,
reference_amb=reference_amb,
reference_ann=reference_ann,
reference_bwt=reference_bwt,
reference_pac=reference_pac,
reference_sa=reference_sa,
reference_dict=reference_dict,
snps_dbsnp=snps_dbsnp,
snps_dbsnp_tbi=snps_dbsnp_tbi,
snps_1000gp=snps_1000gp,
snps_1000gp_tbi=snps_1000gp_tbi,
known_indels=known_indels,
known_indels_tbi=known_indels_tbi,
mills_indels=mills_indels,
mills_indels_tbi=mills_indels_tbi
}
}
scatter (Q in zip(gatk_intervals, transpose([bqsr.out, bqsr.out_bai]))) {
call G4.GATK4_GermlineVariantCaller as vc_gatk {
input:
bam=Q.right[0],
bam_bai=Q.right[1],
intervals=Q.left,
reference=reference,
reference_fai=reference_fai,
reference_amb=reference_amb,
reference_ann=reference_ann,
reference_bwt=reference_bwt,
reference_pac=reference_pac,
reference_sa=reference_sa,
reference_dict=reference_dict,
snps_dbsnp=snps_dbsnp,
snps_dbsnp_tbi=snps_dbsnp_tbi
}
}
call G5.Gatk4GatherVcfs as vc_gatk_merge {
input:
vcfs=vc_gatk.out
}
call B.bgzip as vc_gatk_compress_for_sort {
input:
file=vc_gatk_merge.out
}
call B2.bcftoolssort as vc_gatk_sort_combined {
input:
vcf=vc_gatk_compress_for_sort.out
}
call U.UncompressArchive as vc_gatk_uncompress_for_combine {
input:
file=vc_gatk_sort_combined.out
}
call S.strelkaGermlineVariantCaller as vc_strelka {
input:
bam=bam,
bam_bai=bam_bai,
reference=reference,
reference_fai=reference_fai,
reference_amb=reference_amb,
reference_ann=reference_ann,
reference_bwt=reference_bwt,
reference_pac=reference_pac,
reference_sa=reference_sa,
reference_dict=reference_dict,
intervals=strelka_intervals,
intervals_tbi=strelka_intervals_tbi
}
call G6.GenerateVardictHeaderLines as generate_vardict_headerlines {
input:
reference=reference,
reference_dict=reference_dict
}
scatter (v in vardict_intervals) {
call V.vardictGermlineVariantCaller as vc_vardict {
input:
bam=bam,
bam_bai=bam_bai,
intervals=v,
sample_name=sample_name,
allele_freq_threshold=select_first([vc_vardict_allele_freq_threshold, 0.05]),
header_lines=generate_vardict_headerlines.out,
reference=reference,
reference_fai=reference_fai,
reference_amb=reference_amb,
reference_ann=reference_ann,
reference_bwt=reference_bwt,
reference_pac=reference_pac,
reference_sa=reference_sa,
reference_dict=reference_dict
}
}
call G5.Gatk4GatherVcfs as vc_vardict_merge {
input:
vcfs=vc_vardict.out
}
call B.bgzip as vc_vardict_compress_for_sort {
input:
file=vc_vardict_merge.out
}
call B2.bcftoolssort as vc_vardict_sort_combined {
input:
vcf=vc_vardict_compress_for_sort.out
}
call U.UncompressArchive as vc_vardict_uncompress_for_combine {
input:
file=vc_vardict_sort_combined.out
}
call C.combinevariants as combine_variants {
input:
vcfs=[vc_gatk_uncompress_for_combine.out, vc_strelka.out, vc_vardict_uncompress_for_combine.out],
type=select_first([combine_variants_type, "germline"]),
columns=select_first([combine_variants_columns, ["AC", "AN", "AF", "AD", "DP", "GT"]])
}
call B.bgzip as combined_compress {
input:
file=combine_variants.out
}
call B2.bcftoolssort as combined_sort {
input:
vcf=combined_compress.out
}
call U.UncompressArchive as combined_uncompress {
input:
file=combined_sort.out
}
call A.AddBamStatsGermline as combined_addbamstats {
input:
bam=bam,
bam_bai=bam_bai,
vcf=combined_uncompress.out,
reference=reference,
reference_fai=reference_fai,
reference_amb=reference_amb,
reference_ann=reference_ann,
reference_bwt=reference_bwt,
reference_pac=reference_pac,
reference_sa=reference_sa,
reference_dict=reference_dict
}
output {
File out_performance_summary = performance_summary.performanceSummaryOut
File out_gridss_assembly = vc_gridss.assembly
File out_variants_gridss = vc_gridss.out
File out_variants_gatk = vc_gatk_sort_combined.out
Array[File] out_variants_gatk_split = vc_gatk.out
File out_variants_strelka = vc_strelka.out
File out_variants_vardict = vc_vardict_sort_combined.out
Array[File] out_variants_vardict_split = vc_vardict.out
File out_variants = combined_addbamstats.out
}
}
Common Workflow Language¶
#!/usr/bin/env cwl-runner
class: Workflow
cwlVersion: v1.2
label: WGS Germline (Multi callers) [VARIANTS only]
doc: |
This workflow is a reference pipeline using the Janis Python framework (pipelines assistant).
- Call the appropriate variant callers (GRIDSS / GATK / Strelka / VarDict);
- Merges the variants from GATK / Strelka / VarDict.
- Outputs the final variants in the VCF format.
**Resources**
This pipeline has been tested using the HG38 reference set, available on Google Cloud Storage through:
- https://console.cloud.google.com/storage/browser/genomics-public-data/references/hg38/v0/
This pipeline expects the assembly references to be as they appear in that storage (".fai", ".amb", ".ann", ".bwt", ".pac", ".sa", "^.dict").
The known sites (snps_dbsnp, snps_1000gp, known_indels, mills_indels) should be gzipped and tabix indexed.
requirements:
- class: InlineJavascriptRequirement
- class: StepInputExpressionRequirement
- class: ScatterFeatureRequirement
- class: SubworkflowFeatureRequirement
- class: MultipleInputFeatureRequirement
inputs:
- id: sample_name
doc: Sample name from which to generate the readGroupHeaderLine for BwaMem
type: string
- id: bam
doc: |-
Input indexed bam (+ .bam.bai) to process. You only specify the primary sample.bam, and the index (eg: NA12878.bam.bai) will be picked up automatically.
type: File
secondaryFiles:
- pattern: .bai
- id: reference
doc: |2-
The reference genome from which to align the reads. This requires a number indexes (can be generated with the 'IndexFasta' pipeline This pipeline has been tested using the HG38 reference set.
This pipeline expects the assembly references to be as they appear in the GCP example. For example:
- HG38: https://console.cloud.google.com/storage/browser/genomics-public-data/references/hg38/v0/
- (".fai", ".amb", ".ann", ".bwt", ".pac", ".sa", "^.dict").
type: File
secondaryFiles:
- pattern: .fai
- pattern: .amb
- pattern: .ann
- pattern: .bwt
- pattern: .pac
- pattern: .sa
- pattern: ^.dict
- id: snps_dbsnp
doc: From the GATK resource bundle, passed to BaseRecalibrator as ``known_sites``
type: File
secondaryFiles:
- pattern: .tbi
- id: snps_1000gp
doc: |-
From the GATK resource bundle, passed to BaseRecalibrator as ``known_sites``. Accessible from the HG38 genomics-public-data google cloud bucket: https://console.cloud.google.com/storage/browser/genomics-public-data/references/hg38/v0/
type: File
secondaryFiles:
- pattern: .tbi
- id: known_indels
doc: From the GATK resource bundle, passed to BaseRecalibrator as ``known_sites``
type: File
secondaryFiles:
- pattern: .tbi
- id: mills_indels
doc: From the GATK resource bundle, passed to BaseRecalibrator as ``known_sites``
type: File
secondaryFiles:
- pattern: .tbi
- id: gridss_blacklist
doc: |-
BED file containing regions to ignore. For more information, visit: https://github.com/PapenfussLab/gridss#blacklist
type: File
- id: gatk_intervals
doc: List of intervals over which to split the GATK variant calling
type:
type: array
items: File
- id: vardict_intervals
doc: List of intervals over which to split the VarDict variant calling
type:
type: array
items: File
- id: strelka_intervals
doc: An interval for which to restrict the analysis to.
type: File
secondaryFiles:
- pattern: .tbi
- id: vc_vardict_allele_freq_threshold
type: float
default: 0.05
- id: combine_variants_type
doc: germline | somatic
type: string
default: germline
- id: combine_variants_columns
doc: Columns to keep, seperated by space output vcf (unsorted)
type:
type: array
items: string
default:
- AC
- AN
- AF
- AD
- DP
- GT
outputs:
- id: out_performance_summary
doc: A text file of performance summary of bam
type: File
outputSource: performance_summary/performanceSummaryOut
- id: out_gridss_assembly
doc: Assembly returned by GRIDSS
type: File
outputSource: vc_gridss/assembly
- id: out_variants_gridss
doc: Variants from the GRIDSS variant caller
type: File
outputSource: vc_gridss/out
- id: out_variants_gatk
doc: Merged variants from the GATK caller
type: File
outputSource: vc_gatk_sort_combined/out
- id: out_variants_gatk_split
doc: Unmerged variants from the GATK caller (by interval)
type:
type: array
items: File
outputSource: vc_gatk/out
- id: out_variants_strelka
doc: Variants from the Strelka variant caller
type: File
outputSource: vc_strelka/out
- id: out_variants_vardict
doc: Merged variants from the VarDict caller
type: File
outputSource: vc_vardict_sort_combined/out
- id: out_variants_vardict_split
doc: Unmerged variants from the VarDict caller (by interval)
type:
type: array
items: File
outputSource: vc_vardict/out
- id: out_variants
doc: Combined variants from all 3 callers
type: File
outputSource: combined_addbamstats/out
steps:
- id: calculate_performancesummary_genomefile
label: Generate genome for BedtoolsCoverage
in:
- id: reference
source: reference
run: tools/GenerateGenomeFileForBedtoolsCoverage_v0_1_0.cwl
out:
- id: out
- id: performance_summary
label: Performance summary workflow (whole genome)
in:
- id: bam
source: bam
- id: sample_name
source: sample_name
- id: genome_file
source: calculate_performancesummary_genomefile/out
run: tools/PerformanceSummaryGenome_v0_1_0.cwl
out:
- id: performanceSummaryOut
- id: vc_gridss
label: Gridss
in:
- id: bams
source:
- bam
linkMerge: merge_nested
- id: reference
source: reference
- id: blacklist
source: gridss_blacklist
run: tools/gridss_v2_6_2.cwl
out:
- id: out
- id: assembly
- id: bqsr
label: GATK Base Recalibration on Bam
in:
- id: bam
source: bam
- id: intervals
source: gatk_intervals
- id: reference
source: reference
- id: snps_dbsnp
source: snps_dbsnp
- id: snps_1000gp
source: snps_1000gp
- id: known_indels
source: known_indels
- id: mills_indels
source: mills_indels
scatter:
- intervals
run: tools/GATKBaseRecalBQSRWorkflow_4_1_3.cwl
out:
- id: out
- id: vc_gatk
label: GATK4 Germline Variant Caller
in:
- id: bam
source: bqsr/out
- id: intervals
source: gatk_intervals
- id: reference
source: reference
- id: snps_dbsnp
source: snps_dbsnp
scatter:
- intervals
- bam
scatterMethod: dotproduct
run: tools/GATK4_GermlineVariantCaller_4_1_3_0.cwl
out:
- id: variants
- id: out_bam
- id: out
- id: vc_gatk_merge
label: 'GATK4: Gather VCFs'
in:
- id: vcfs
source: vc_gatk/out
run: tools/Gatk4GatherVcfs_4_1_3_0.cwl
out:
- id: out
- id: vc_gatk_compress_for_sort
label: BGZip
in:
- id: file
source: vc_gatk_merge/out
run: tools/bgzip_1_2_1.cwl
out:
- id: out
- id: vc_gatk_sort_combined
label: 'BCFTools: Sort'
in:
- id: vcf
source: vc_gatk_compress_for_sort/out
run: tools/bcftoolssort_v1_9.cwl
out:
- id: out
- id: vc_gatk_uncompress_for_combine
label: UncompressArchive
in:
- id: file
source: vc_gatk_sort_combined/out
run: tools/UncompressArchive_v1_0_0.cwl
out:
- id: out
- id: vc_strelka
label: Strelka Germline Variant Caller
in:
- id: bam
source: bam
- id: reference
source: reference
- id: intervals
source: strelka_intervals
run: tools/strelkaGermlineVariantCaller_v0_1_1.cwl
out:
- id: sv
- id: variants
- id: out
- id: generate_vardict_headerlines
label: GenerateVardictHeaderLines
in:
- id: reference
source: reference
run: tools/GenerateVardictHeaderLines_v0_1_0.cwl
out:
- id: out
- id: vc_vardict
label: Vardict Germline Variant Caller
in:
- id: bam
source: bam
- id: intervals
source: vardict_intervals
- id: sample_name
source: sample_name
- id: allele_freq_threshold
source: vc_vardict_allele_freq_threshold
- id: header_lines
source: generate_vardict_headerlines/out
- id: reference
source: reference
scatter:
- intervals
run: tools/vardictGermlineVariantCaller_v0_1_1.cwl
out:
- id: variants
- id: out
- id: vc_vardict_merge
label: 'GATK4: Gather VCFs'
in:
- id: vcfs
source: vc_vardict/out
run: tools/Gatk4GatherVcfs_4_1_3_0.cwl
out:
- id: out
- id: vc_vardict_compress_for_sort
label: BGZip
in:
- id: file
source: vc_vardict_merge/out
run: tools/bgzip_1_2_1.cwl
out:
- id: out
- id: vc_vardict_sort_combined
label: 'BCFTools: Sort'
in:
- id: vcf
source: vc_vardict_compress_for_sort/out
run: tools/bcftoolssort_v1_9.cwl
out:
- id: out
- id: vc_vardict_uncompress_for_combine
label: UncompressArchive
in:
- id: file
source: vc_vardict_sort_combined/out
run: tools/UncompressArchive_v1_0_0.cwl
out:
- id: out
- id: combine_variants
label: Combine Variants
in:
- id: vcfs
source:
- vc_gatk_uncompress_for_combine/out
- vc_strelka/out
- vc_vardict_uncompress_for_combine/out
- id: type
source: combine_variants_type
- id: columns
source: combine_variants_columns
run: tools/combinevariants_0_0_8.cwl
out:
- id: out
- id: combined_compress
label: BGZip
in:
- id: file
source: combine_variants/out
run: tools/bgzip_1_2_1.cwl
out:
- id: out
- id: combined_sort
label: 'BCFTools: Sort'
in:
- id: vcf
source: combined_compress/out
run: tools/bcftoolssort_v1_9.cwl
out:
- id: out
- id: combined_uncompress
label: UncompressArchive
in:
- id: file
source: combined_sort/out
run: tools/UncompressArchive_v1_0_0.cwl
out:
- id: out
- id: combined_addbamstats
label: Annotate Bam Stats to Germline Vcf Workflow
in:
- id: bam
source: bam
- id: vcf
source: combined_uncompress/out
- id: reference
source: reference
run: tools/AddBamStatsGermline_v0_1_0.cwl
out:
- id: out
id: WGSGermlineMultiCallersVariantsOnly