align.yaml 1.98 KB
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align:
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  - bwa[tool]:
    - single[read_end]:
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        - bwa_align_single:
            inputs:
              - ref_genome
              - download_1.fastq
            additional_inputs:
              - ref_genome.amb
              - ref_genome.ann
              - ref_genome.bwt
              - ref_genome.pac
              - ref_genome.sa
            outputs:
              - bwa.sai
        - bwa_sai_to_sam:
            inputs:
              - ref_genome.fa
              - bwa.sai
              - download_1.fastq
            additional_inputs: null
            outputs:
              - align.sam
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      paired[read_end]:
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        - bwa_align_paired:
            inputs:
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              - ref_genome
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              - download_1.fastq
              - download_2.fastq
            additional_inputs:
              - ref_genome.amb
              - ref_genome.ann
              - ref_genome.bwt
              - ref_genome.pac
              - ref_genome.sa
            outputs:
              - align.sam
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    bowtie2[tool]:
    - single[read_end]:
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        - bowtie2_align_single:
            inputs:
              - ref_genome
              - download_1.fastq
            additional_inputs:
                - ref_genome.1.bt2
                - ref_genome.2.bt2
                - ref_genome.3.bt2
                - ref_genome.4.bt2
                - ref_genome.rev.1.bt2
                - ref_genome.rev.2.bt2
            outputs:
              - align.sam
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      paired[read_end]:
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        - bowtie2_align_paired:
            inputs:
              - ref_genome
              - download_1.fastq
              - download_2.fastq
            additional_inputs:
              - ref_genome.1.bt2
              - ref_genome.2.bt2
              - ref_genome.3.bt2
              - ref_genome.4.bt2
              - ref_genome.rev.1.bt2
              - ref_genome.rev.2.bt2
            outputs:
              - align.sam
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  - samtools_sam_to_bam:
      inputs:
        - align.sam
      additional_inputs: null
      outputs:
        - align.bam