class: Workflow cwlVersion: v1.0 hints: [] inputs: - id: alignment_rec type: fields: - name: resources type: string - name: description type: string - name: config__algorithm__align_split_size type: - 'null' - string - boolean - long - name: files type: - 'null' - items: File type: array - name: config__algorithm__trim_reads type: - string - 'null' - boolean - name: reference__fasta__base type: File - name: config__algorithm__adapters type: - 'null' - items: 'null' type: array - name: rgnames__lb type: - 'null' - string - name: rgnames__rg type: string - name: config__algorithm__umi_type type: - 'null' - string - name: rgnames__lane type: string - name: reference__bwa__indexes type: - 'null' - File - name: config__algorithm__bam_clean type: - string - 'null' - boolean - name: config__algorithm__aligner type: - 'null' - string - boolean - name: reference__minimap2__indexes type: - 'null' - items: 'null' type: array - name: rgnames__pl type: string - name: rgnames__pu type: string - name: config__algorithm__mark_duplicates type: - string - 'null' - boolean - name: analysis type: string - name: rgnames__sample type: string name: alignment_rec type: record outputs: - id: align_bam outputSource: merge_split_alignments/align_bam secondaryFiles: - .bai type: - File - 'null' - id: work_bam_plus__disc outputSource: merge_split_alignments/work_bam_plus__disc secondaryFiles: - .bai type: - File - 'null' - id: work_bam_plus__sr outputSource: merge_split_alignments/work_bam_plus__sr secondaryFiles: - .bai type: - File - 'null' - id: hla__fastq outputSource: merge_split_alignments/hla__fastq type: - 'null' - items: File type: array - id: umi_bam outputSource: merge_split_alignments/umi_bam secondaryFiles: - .bai type: - File - 'null' - id: config__algorithm__rawumi_avg_cov outputSource: merge_split_alignments/config__algorithm__rawumi_avg_cov type: - int - 'null' requirements: - class: EnvVarRequirement envDef: - envName: MPLCONFIGDIR envValue: . - class: ScatterFeatureRequirement - class: SubworkflowFeatureRequirement steps: - id: prep_align_inputs in: - id: alignment_rec source: alignment_rec out: - id: process_alignment_rec run: steps/prep_align_inputs.cwl - id: process_alignment in: - id: alignment_rec source: alignment_rec - id: process_alignment_rec source: prep_align_inputs/process_alignment_rec out: - id: work_bam - id: align_bam - id: hla__fastq - id: work_bam_plus__disc - id: work_bam_plus__sr - id: config__algorithm__rawumi_avg_cov - id: umi_bam run: steps/process_alignment.cwl scatter: - process_alignment_rec scatterMethod: dotproduct - id: merge_split_alignments in: - id: alignment_rec source: alignment_rec - id: work_bam source: process_alignment/work_bam - id: align_bam_toolinput source: process_alignment/align_bam - id: work_bam_plus__disc_toolinput source: process_alignment/work_bam_plus__disc - id: work_bam_plus__sr_toolinput source: process_alignment/work_bam_plus__sr - id: hla__fastq_toolinput source: process_alignment/hla__fastq - id: umi_bam_toolinput source: process_alignment/umi_bam - id: config__algorithm__rawumi_avg_cov_toolinput source: process_alignment/config__algorithm__rawumi_avg_cov out: - id: align_bam - id: work_bam_plus__disc - id: work_bam_plus__sr - id: hla__fastq - id: umi_bam - id: config__algorithm__rawumi_avg_cov run: steps/merge_split_alignments.cwl