class: Workflow
cwlVersion: v1.0
hints: []
inputs:
- id: config__algorithm__align_split_size
type:
items:
- 'null'
- string
type: array
- id: files
secondaryFiles:
- .bai
type:
items:
items: File
type: array
type: array
- id: config__algorithm__trim_reads
type:
items:
- string
- 'null'
- boolean
type: array
- id: reference__fasta__base
secondaryFiles:
- .fai
- ^.dict
type:
items: File
type: array
- id: resources
type:
items: string
type: array
- id: config__algorithm__variantcaller
type:
items:
items: string
type: array
type: array
- id: config__algorithm__adapters
type:
items:
- 'null'
- string
- items:
- 'null'
- string
type: array
type: array
- id: reference__snpeff__GRCh37_75
type:
items: File
type: array
- id: config__algorithm__coverage_interval
type:
items:
- 'null'
- string
type: array
- id: genome_resources__rnaseq__gene_bed
type:
items: File
type: array
- id: genome_resources__variation__train_hapmap
secondaryFiles:
- .tbi
type:
items: File
type: array
- id: rgnames__lb
type:
items:
- 'null'
- string
type: array
- id: genome_resources__variation__encode_blacklist
secondaryFiles:
- .tbi
type:
items: File
type: array
- id: rgnames__rg
type:
items: string
type: array
- id: metadata__batch
type:
items:
- 'null'
- string
type: array
- id: rgnames__lane
type:
items: string
type: array
- id: genome_resources__variation__lcr
secondaryFiles:
- .tbi
type:
items: File
type: array
- id: config__algorithm__nomap_split_targets
type:
items: long
type: array
- id: vrn_file
type:
items:
- 'null'
- string
type: array
- id: reference__twobit
type:
items: File
type: array
- id: config__algorithm__bam_clean
type:
items:
- string
- 'null'
- boolean
type: array
- id: config__algorithm__nomap_split_size
type:
items: long
type: array
- id: config__algorithm__validate
secondaryFiles:
- .tbi
type:
items: File
type: array
- id: description
type:
items: string
type: array
- id: config__algorithm__validate_regions
type:
items: File
type: array
- id: config__algorithm__aligner
type:
items: string
type: array
- id: reference__minimap2__indexes
type:
items:
- 'null'
- string
- items:
- 'null'
- string
type: array
type: array
- id: rgnames__pl
type:
items: string
type: array
- id: genome_build
type:
items: string
type: array
- id: rgnames__pu
type:
items: string
type: array
- id: config__algorithm__recalibrate
type:
items:
- string
- 'null'
- boolean
type: array
- id: metadata__phenotype
type:
items: string
type: array
- id: genome_resources__aliases__human
type:
items:
- string
- 'null'
- boolean
type: array
- id: config__algorithm__tools_off
type:
items:
items: string
type: array
type: array
- id: genome_resources__variation__dbsnp
secondaryFiles:
- .tbi
type:
items: File
type: array
- id: config__algorithm__mark_duplicates
type:
items:
- string
- 'null'
- boolean
type: array
- id: genome_resources__variation__polyx
secondaryFiles:
- .tbi
type:
items: File
type: array
- id: genome_resources__variation__cosmic
secondaryFiles:
- .tbi
type:
items: File
type: array
- id: reference__genome_context
secondaryFiles:
- .tbi
type:
items:
items: File
type: array
type: array
- id: config__algorithm__qc
type:
items:
items: string
type: array
type: array
- id: analysis
type:
items: string
type: array
- id: rgnames__sample
type:
items: string
type: array
- id: config__algorithm__tools_on
type:
items:
- 'null'
- string
- items:
- 'null'
- string
type: array
type: array
- id: config__algorithm__effects
type:
items:
- string
- 'null'
- boolean
type: array
- id: config__algorithm__variant_regions
type:
items: File
type: array
- id: genome_resources__aliases__ensembl
type:
items: string
type: array
- id: config__algorithm__exclude_regions
type:
items:
- 'null'
- string
- items:
- 'null'
- string
type: array
type: array
- id: reference__rtg
type:
items: File
type: array
- id: genome_resources__variation__train_indels
secondaryFiles:
- .tbi
type:
items: File
type: array
- id: genome_resources__aliases__snpeff
type:
items: string
type: array
outputs:
- id: align_bam
outputSource: postprocess_alignment/align_bam
type:
items:
- File
- 'null'
type: array
- id: regions__sample_callable
outputSource: postprocess_alignment/regions__sample_callable
type:
items:
- File
- 'null'
type: array
- id: validate__grading_summary
outputSource: summarize_vc/validate__grading_summary
type:
items:
- File
- 'null'
type: array
- id: variants__calls
outputSource: summarize_vc/variants__calls
type:
items:
items:
- File
- 'null'
type: array
type: array
- id: variants__gvcf
outputSource: summarize_vc/variants__gvcf
type:
items:
- 'null'
- items:
- File
- 'null'
type: array
type: array
- id: summary__multiqc
outputSource: multiqc_summary/summary__multiqc
type:
items:
- File
- 'null'
type: array
- id: rgnames__sample_out
outputSource: rgnames__sample
type:
items: string
type: array
requirements:
- class: EnvVarRequirement
envDef:
- envName: MPLCONFIGDIR
envValue: .
- class: ScatterFeatureRequirement
- class: SubworkflowFeatureRequirement
steps:
- id: alignment_to_rec
in:
- id: files
source: files
- id: analysis
source: analysis
- id: config__algorithm__align_split_size
source: config__algorithm__align_split_size
- id: reference__fasta__base
source: reference__fasta__base
- id: rgnames__pl
source: rgnames__pl
- id: rgnames__sample
source: rgnames__sample
- id: rgnames__pu
source: rgnames__pu
- id: rgnames__lane
source: rgnames__lane
- id: rgnames__rg
source: rgnames__rg
- id: rgnames__lb
source: rgnames__lb
- id: reference__minimap2__indexes
source: reference__minimap2__indexes
- id: config__algorithm__aligner
source: config__algorithm__aligner
- id: config__algorithm__trim_reads
source: config__algorithm__trim_reads
- id: config__algorithm__adapters
source: config__algorithm__adapters
- id: config__algorithm__bam_clean
source: config__algorithm__bam_clean
- id: config__algorithm__mark_duplicates
source: config__algorithm__mark_duplicates
- id: resources
source: resources
- id: description
source: description
out:
- id: alignment_rec
run: steps/alignment_to_rec.cwl
- id: alignment
in:
- id: alignment_rec
source: alignment_to_rec/alignment_rec
out:
- id: align_bam
- id: work_bam_plus__disc
- id: work_bam_plus__sr
- id: hla__fastq
run: wf-alignment.cwl
scatter:
- alignment_rec
scatterMethod: dotproduct
- id: prep_samples_to_rec
in:
- id: config__algorithm__variant_regions
source: config__algorithm__variant_regions
- id: reference__fasta__base
source: reference__fasta__base
- id: resources
source: resources
- id: description
source: description
out:
- id: prep_samples_rec
run: steps/prep_samples_to_rec.cwl
- id: prep_samples
in:
- id: prep_samples_rec
source: prep_samples_to_rec/prep_samples_rec
out:
- id: config__algorithm__variant_regions
- id: config__algorithm__variant_regions_merged
- id: config__algorithm__variant_regions_orig
- id: config__algorithm__coverage
- id: config__algorithm__coverage_merged
- id: config__algorithm__coverage_orig
- id: config__algorithm__seq2c_bed_ready
run: steps/prep_samples.cwl
scatter:
- prep_samples_rec
scatterMethod: dotproduct
- id: postprocess_alignment_to_rec
in:
- id: align_bam
source: alignment/align_bam
- id: config__algorithm__coverage_interval
source: config__algorithm__coverage_interval
- id: config__algorithm__exclude_regions
source: config__algorithm__exclude_regions
- id: config__algorithm__variant_regions
source: prep_samples/config__algorithm__variant_regions
- id: config__algorithm__variant_regions_merged
source: prep_samples/config__algorithm__variant_regions_merged
- id: config__algorithm__variant_regions_orig
source: prep_samples/config__algorithm__variant_regions_orig
- id: config__algorithm__coverage
source: prep_samples/config__algorithm__coverage
- id: config__algorithm__coverage_merged
source: prep_samples/config__algorithm__coverage_merged
- id: config__algorithm__coverage_orig
source: prep_samples/config__algorithm__coverage_orig
- id: config__algorithm__seq2c_bed_ready
source: prep_samples/config__algorithm__seq2c_bed_ready
- id: config__algorithm__recalibrate
source: config__algorithm__recalibrate
- id: config__algorithm__tools_on
source: config__algorithm__tools_on
- id: genome_resources__rnaseq__gene_bed
source: genome_resources__rnaseq__gene_bed
- id: genome_resources__variation__dbsnp
source: genome_resources__variation__dbsnp
- id: genome_resources__variation__lcr
source: genome_resources__variation__lcr
- id: genome_resources__variation__polyx
source: genome_resources__variation__polyx
- id: genome_resources__variation__encode_blacklist
source: genome_resources__variation__encode_blacklist
- id: reference__twobit
source: reference__twobit
- id: reference__fasta__base
source: reference__fasta__base
- id: resources
source: resources
- id: description
source: description
out:
- id: postprocess_alignment_rec
run: steps/postprocess_alignment_to_rec.cwl
- id: postprocess_alignment
in:
- id: postprocess_alignment_rec
source: postprocess_alignment_to_rec/postprocess_alignment_rec
out:
- id: config__algorithm__coverage_interval
- id: config__algorithm__variant_regions
- id: config__algorithm__variant_regions_merged
- id: config__algorithm__variant_regions_orig
- id: config__algorithm__coverage
- id: config__algorithm__coverage_merged
- id: config__algorithm__coverage_orig
- id: config__algorithm__seq2c_bed_ready
- id: regions__callable
- id: regions__sample_callable
- id: regions__nblock
- id: depth__samtools__stats
- id: depth__samtools__idxstats
- id: depth__variant_regions__regions
- id: depth__variant_regions__dist
- id: depth__sv_regions__regions
- id: depth__sv_regions__dist
- id: depth__coverage__regions
- id: depth__coverage__dist
- id: depth__coverage__thresholds
- id: align_bam
run: steps/postprocess_alignment.cwl
scatter:
- postprocess_alignment_rec
scatterMethod: dotproduct
- id: combine_sample_regions
in:
- id: regions__callable
source: postprocess_alignment/regions__callable
- id: regions__nblock
source: postprocess_alignment/regions__nblock
- id: metadata__batch
source: metadata__batch
- id: config__algorithm__nomap_split_size
source: config__algorithm__nomap_split_size
- id: config__algorithm__nomap_split_targets
source: config__algorithm__nomap_split_targets
- id: reference__fasta__base
source: reference__fasta__base
- id: resources
source: resources
- id: description
source: description
out:
- id: config__algorithm__callable_regions
- id: config__algorithm__non_callable_regions
- id: config__algorithm__callable_count
run: steps/combine_sample_regions.cwl
- id: batch_for_variantcall
in:
- id: analysis
source: analysis
- id: genome_build
source: genome_build
- id: align_bam
source: postprocess_alignment/align_bam
- id: vrn_file
source: vrn_file
- id: config__algorithm__callable_regions
source: combine_sample_regions/config__algorithm__callable_regions
- id: metadata__batch
source: metadata__batch
- id: metadata__phenotype
source: metadata__phenotype
- id: regions__sample_callable
source: postprocess_alignment/regions__sample_callable
- id: config__algorithm__variantcaller
source: config__algorithm__variantcaller
- id: config__algorithm__coverage_interval
source: postprocess_alignment/config__algorithm__coverage_interval
- id: config__algorithm__effects
source: config__algorithm__effects
- id: config__algorithm__exclude_regions
source: config__algorithm__exclude_regions
- id: config__algorithm__variant_regions
source: postprocess_alignment/config__algorithm__variant_regions
- id: config__algorithm__validate
source: config__algorithm__validate
- id: config__algorithm__validate_regions
source: config__algorithm__validate_regions
- id: config__algorithm__tools_on
source: config__algorithm__tools_on
- id: config__algorithm__tools_off
source: config__algorithm__tools_off
- id: reference__fasta__base
source: reference__fasta__base
- id: reference__twobit
source: reference__twobit
- id: reference__rtg
source: reference__rtg
- id: reference__genome_context
source: reference__genome_context
- id: genome_resources__variation__cosmic
source: genome_resources__variation__cosmic
- id: genome_resources__variation__dbsnp
source: genome_resources__variation__dbsnp
- id: genome_resources__variation__lcr
source: genome_resources__variation__lcr
- id: genome_resources__variation__polyx
source: genome_resources__variation__polyx
- id: genome_resources__variation__encode_blacklist
source: genome_resources__variation__encode_blacklist
- id: genome_resources__variation__train_hapmap
source: genome_resources__variation__train_hapmap
- id: genome_resources__variation__train_indels
source: genome_resources__variation__train_indels
- id: genome_resources__aliases__ensembl
source: genome_resources__aliases__ensembl
- id: genome_resources__aliases__human
source: genome_resources__aliases__human
- id: genome_resources__aliases__snpeff
source: genome_resources__aliases__snpeff
- id: reference__snpeff__GRCh37_75
source: reference__snpeff__GRCh37_75
- id: resources
source: resources
- id: description
source: description
out:
- id: batch_rec
run: steps/batch_for_variantcall.cwl
- id: variantcall
in:
- id: batch_rec
source: batch_for_variantcall/batch_rec
out:
- id: vc_rec
run: wf-variantcall.cwl
scatter:
- batch_rec
scatterMethod: dotproduct
- id: summarize_vc
in:
- id: vc_rec
source: variantcall/vc_rec
out:
- id: variants__calls
- id: variants__gvcf
- id: variants__samples
- id: validate__grading_summary
- id: validate__grading_plots
run: steps/summarize_vc.cwl
- id: qc_to_rec
in:
- id: align_bam
source: postprocess_alignment/align_bam
- id: analysis
source: analysis
- id: reference__fasta__base
source: reference__fasta__base
- id: config__algorithm__tools_on
source: config__algorithm__tools_on
- id: config__algorithm__tools_off
source: config__algorithm__tools_off
- id: genome_build
source: genome_build
- id: config__algorithm__qc
source: config__algorithm__qc
- id: metadata__batch
source: metadata__batch
- id: config__algorithm__coverage_interval
source: postprocess_alignment/config__algorithm__coverage_interval
- id: depth__variant_regions__regions
source: postprocess_alignment/depth__variant_regions__regions
- id: depth__variant_regions__dist
source: postprocess_alignment/depth__variant_regions__dist
- id: depth__samtools__stats
source: postprocess_alignment/depth__samtools__stats
- id: depth__samtools__idxstats
source: postprocess_alignment/depth__samtools__idxstats
- id: depth__sv_regions__regions
source: postprocess_alignment/depth__sv_regions__regions
- id: depth__sv_regions__dist
source: postprocess_alignment/depth__sv_regions__dist
- id: depth__coverage__regions
source: postprocess_alignment/depth__coverage__regions
- id: depth__coverage__dist
source: postprocess_alignment/depth__coverage__dist
- id: depth__coverage__thresholds
source: postprocess_alignment/depth__coverage__thresholds
- id: config__algorithm__variant_regions
source: postprocess_alignment/config__algorithm__variant_regions
- id: config__algorithm__variant_regions_merged
source: postprocess_alignment/config__algorithm__variant_regions_merged
- id: config__algorithm__coverage
source: postprocess_alignment/config__algorithm__coverage
- id: config__algorithm__coverage_merged
source: postprocess_alignment/config__algorithm__coverage_merged
- id: variants__samples
source: summarize_vc/variants__samples
- id: resources
source: resources
- id: description
source: description
out:
- id: qc_rec
run: steps/qc_to_rec.cwl
- id: pipeline_summary
in:
- id: qc_rec
source: qc_to_rec/qc_rec
out:
- id: qcout_rec
run: steps/pipeline_summary.cwl
scatter:
- qc_rec
scatterMethod: dotproduct
- id: multiqc_summary
in:
- id: qcout_rec
source: pipeline_summary/qcout_rec
out:
- id: summary__multiqc
run: steps/multiqc_summary.cwl