class: Workflow cwlVersion: v1.0 hints: [] inputs: - id: config__algorithm__align_split_size type: items: - string - 'null' - boolean type: array - id: files secondaryFiles: - .gbi 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: 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__GRCh38_86 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: rgnames__lb type: items: - 'null' - string type: array - id: genome_resources__variation__encode_blacklist type: items: - 'null' - string 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: metadata__phenotype type: items: string type: array - id: config__algorithm__nomap_split_targets type: items: long 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: vrn_file type: items: - 'null' - string type: array - id: config__algorithm__recalibrate type: items: - string - 'null' - boolean type: array - id: config__algorithm__coverage type: items: File 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: rgnames__pu type: items: string type: array - id: genome_resources__variation__polyx secondaryFiles: - .tbi type: items: File type: array - id: genome_resources__variation__cosmic type: items: - 'null' - string 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 type: array - id: config__algorithm__variant_regions type: items: File type: array - id: resources type: items: string 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__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 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: description source: description - id: resources source: resources 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: hla__fastq - id: work_bam_plus__disc - id: work_bam_plus__sr run: wf-alignment.cwl scatter: - alignment_rec scatterMethod: dotproduct - id: prep_samples_to_rec in: - id: config__algorithm__coverage source: config__algorithm__coverage - id: config__algorithm__variant_regions source: config__algorithm__variant_regions - id: reference__fasta__base source: reference__fasta__base - id: description source: description - id: resources source: resources 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: description source: description - id: resources source: resources 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: description source: description - id: resources source: resources 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__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__GRCh38_86 source: reference__snpeff__GRCh38_86 - id: description source: description - id: resources source: resources 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: description source: description - id: resources source: resources 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