class: Workflow cwlVersion: v1.0 id: topmed_alignment doc: >- A CWL wrapper of the TopMed alignment workflow described here: https://github.com/statgen/docker-alignment Tool Author: Hyun Min Kang (hmkang@umich.edu) and Adrian Tan (atks@umich.edu) Wrapper Author: Marko Zecevic (marko.zecevic@sbgenomics.com) label: TOPMed Alignment $namespaces: sbg: 'https://sevenbridges.com' inputs: - id: input_file 'sbg:fileTypes': CRAM type: File label: Input CRAM file 'sbg:x': -253.4855499267578 'sbg:y': 25.186986923217773 - id: bwa_index 'sbg:fileTypes': TAR type: File label: BWA Index 'sbg:x': 114.04255676269531 'sbg:y': 179.9574432373047 - id: reference_genome 'sbg:fileTypes': 'FA, FASTA' type: File label: Reference for output CRAM compressing 'sbg:x': -106.77165222167969 'sbg:y': -187.8012237548828 - id: dbsnp 'sbg:fileTypes': 'VCF, VCF.GZ' type: File? label: dbSNP VCF file 'sbg:x': 400 'sbg:y': 222 - id: decomp_ref 'sbg:fileTypes': 'FASTA, FA' type: File? label: Reference for input CRAM decompressing 'sbg:x': -152.35092163085938 'sbg:y': 139.45030212402344 - id: threads type: int? label: Number of threads - id: ram_min type: int? label: Minimum amount of RAM - id: cores_min type: int? label: Minimum number of cores outputs: - id: output outputSource: topmed_post_align/output 'sbg:fileTypes': CRAM type: File? label: Output CRAM file 'sbg:x': 861 'sbg:y': -72 steps: - id: topmed_pre_align in: - id: input_file source: input_file - id: decomp_ref source: decomp_ref - id: comp_ref source: reference_genome - id: threads source: threads default: 1 - id: ram_min source: ram_min default: 7500 - id: cores_min source: cores_min default: 8 out: - id: fastq - id: list run: steps/pre-align.cwl label: Pre-align 1.0 'sbg:x': 130.828125 'sbg:y': 0 - id: topmed_align in: - id: reference source: bwa_index - id: fastq source: topmed_pre_align/fastq - id: list source: topmed_pre_align/list - id: ram_min source: ram_min default: 14000 - id: cores_min source: cores_min default: 8 out: - id: cram run: steps/align.cwl label: Align 1.0 scatter: - fastq scatterMethod: dotproduct 'sbg:x': 307 'sbg:y': 63.021278381347656 - id: samtools_sort in: - id: reference source: reference_genome - id: input_file source: topmed_align/cram - id: threads source: threads default: 1 - id: ram_min source: ram_min default: 7000 - id: cores_min source: cores_min default: 2 out: - id: output run: steps/samtools-sort.cwl label: SAMtools Sort scatter: - input_file scatterMethod: dotproduct 'sbg:x': 482.89361572265625 'sbg:y': -1.872340440750122 - id: topmed_post_align in: - id: reference source: reference_genome - id: dbsnp source: dbsnp - id: alignment_files source: samtools_sort/output - id: input_cram source: input_file - id: threads source: threads default: 1 - id: ram_min source: ram_min default: 7500 - id: cores_min source: cores_min default: 8 out: - id: output run: steps/post-align.cwl label: Post-align 'sbg:x': 668.5106811523438 'sbg:y': 8.829793930053711 hints: - class: 'sbg:maxNumberOfParallelInstances' value: '8' requirements: - class: ScatterFeatureRequirement - class: MultipleInputFeatureRequirement 'dct:creator': 'foaf:mbox': 'mailto:support@sbgenomics.com' 'foaf:name': Seven Bridges 'sbg:categories': - Alignment 'sbg:links': - id: 'https://github.com/statgen/docker-alignment' label: github 'sbg:toolAuthor': Hyun Min Kang (hmkang@umich.edu) and Adrian Tan (atks@umich.edu) 'sbg:wrapperAuthor': Marko Zecevic (marko.zecevic@sbgenomics.com)