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main-NA12878-platinum-chr20.cwl
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main-NA12878-platinum-chr20.cwl
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class: Workflow
cwlVersion: v1.0
hints: []
inputs:
- id: config__algorithm__align_split_size
type:
items: 'null'
type: array
- id: config__algorithm__validate
type:
items: File
type: array
- id: reference__fasta__base
type:
items: File
type: array
- id: genome_resources__variation__lcr
type:
items: File
type: array
- id: reference__snpeff
type:
items: File
type: array
- id: config__algorithm__variantcaller
type:
items:
items: string
type: array
type: array
- id: genome_resources__rnaseq__transcripts_mask
type:
items: File
type: array
- id: genome_resources__variation__train_1000g
type:
items: File
type: array
- id: config__algorithm__coverage_interval
type:
items: 'null'
type: array
- id: genome_resources__variation__qsignature
type:
items: File
type: array
- id: genome_resources__variation__train_hapmap
type:
items: File
type: array
- id: rgnames__lb
type:
items: 'null'
type: array
- id: rgnames__rg
type:
items: string
type: array
- id: config__algorithm__realign
type:
items: string
type: array
- id: metadata__batch
type:
items: 'null'
type: array
- id: rgnames__lane
type:
items: string
type: array
- id: config__algorithm__nomap_split_targets
type:
items: long
type: array
- id: genome_resources__variation__sv_repeat
type:
items: File
type: array
- id: reference__bwa__indexes
type:
items: File
type: array
- id: config__algorithm__nomap_split_size
type:
items: long
type: array
- id: files
type:
items:
items: File
type: array
type: array
- id: genome_resources__rnaseq__dexseq
type:
items: File
type: array
- id: description
type:
items: string
type: array
- id: config__algorithm__validate_regions
type:
items: File
type: array
- id: genome_resources__rnaseq__transcriptome_index__tophat
type:
items: string
type: array
- id: config__algorithm__aligner
type:
items: string
type: array
- id: genome_resources__variation__train_omni
type:
items: File
type: array
- id: rgnames__pl
type:
items: string
type: array
- id: genome_build
type:
items: string
type: array
- id: vrn_file
type:
items: 'null'
type: array
- id: config__algorithm__recalibrate
type:
items: string
type: array
- id: metadata__phenotype
type:
items: string
type: array
- id: genome_resources__rnaseq__transcripts
type:
items: File
type: array
- id: genome_resources__aliases__human
type:
items: string
type: array
- id: config__algorithm__tools_off
type:
items:
items: string
type: array
type: array
- id: genome_resources__variation__dbsnp
type:
items: File
type: array
- id: config__algorithm__mark_duplicates
type:
items: string
type: array
- id: rgnames__pu
type:
items: string
type: array
- id: reference__viral
type:
items:
items: 'null'
type: array
type: array
- id: genome_resources__version
type:
items: long
type: array
- id: genome_resources__variation__cosmic
type:
items: 'null'
type: array
- id: genome_resources__rnaseq__refflat
type:
items: File
type: array
- id: reference__genome_context
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:
items: string
type: array
type: array
- id: config__algorithm__effects
type:
items: string
type: array
- id: config__algorithm__variant_regions
type:
items: 'null'
type: array
- id: genome_resources__aliases__ensembl
type:
items: string
type: array
- id: reference__rtg
type:
items: File
type: array
- id: genome_resources__variation__train_indels
type:
items: File
type: array
- id: genome_resources__aliases__snpeff
type:
items: string
type: array
- id: config__algorithm__archive
type:
items:
items: 'null'
type: array
type: array
outputs:
- id: align_bam
outputSource: alignment/align_bam
type:
items: File
type: array
- id: summary__multiqc
outputSource: multiqc_summary/summary__multiqc
type:
items:
- File
- 'null'
type: array
- id: validate__grading_summary
outputSource: summarize_grading_vc/validate__grading_summary
type:
items:
- File
- 'null'
type: array
requirements:
- class: EnvVarRequirement
envDef:
- envName: MPLCONFIGDIR
envValue: .
- class: ScatterFeatureRequirement
- class: SubworkflowFeatureRequirement
steps:
- id: alignment_to_rec
in:
- id: files
source: files
- 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__bwa__indexes
source: reference__bwa__indexes
- id: config__algorithm__aligner
source: config__algorithm__aligner
- id: config__algorithm__mark_duplicates
source: config__algorithm__mark_duplicates
- 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: 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__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: reference__fasta__base
source: reference__fasta__base
- 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: regions__highdepth
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: 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: 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: qc_to_rec
in:
- id: align_bam
source: alignment/align_bam
- id: analysis
source: analysis
- id: reference__fasta__base
source: reference__fasta__base
- id: genome_build
source: genome_build
- id: config__algorithm__coverage_interval
source: postprocess_alignment/config__algorithm__coverage_interval
- id: config__algorithm__tools_on
source: config__algorithm__tools_on
- id: config__algorithm__tools_off
source: config__algorithm__tools_off
- id: config__algorithm__qc
source: config__algorithm__qc
- 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: 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
- id: batch_for_variantcall
in:
- id: analysis
source: analysis
- id: genome_build
source: genome_build
- id: align_bam
source: alignment/align_bam
- 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__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__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: 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_grading_vc
in:
- id: vc_rec
source: variantcall/vc_rec
out:
- id: validate__grading_summary
- id: validate__grading_plots
run: steps/summarize_grading_vc.cwl