coastguard.yml

settings:
  environ:
    working_directory: .
    temporary_directory: ''
    output_directory: ''
    custom:
      Baywatch:
        name: 'DGE/DTU pipeline'
        description: |
            This pipeline uses snakemake, minimap2, salmon, edgeR, DEXSeq and stageR to automate simple differential gene expression and differential transcript usage workflows on long read data.
        fields:
        - label: Transcriptome fasta
          description: Transcriptome fasta
          path: workflow.data.transcriptome.path
          fieldType: file
        - label: Annotation GFF/GTF
          description: Annotation GFF/GTF
          path: workflow.data.annotation.path
          fieldType: file
        - label: Minimap2 indexing options
          description: Minimap2 indexing options
          path: workflow.data.minimap_index_opts.path
          fieldType: string
          value: ''
        - label: Minimap2 mapping options
          description: Minimap2 mapping options
          path: workflow.data.minimap2_opts.path
          fieldType: string
          value: ''
        - label: Maximum secondary alignments
          description: Maximum secondary alignments
          path: workflow.data.maximum_secondary.path
          fieldType: number
          value: 100
        - label: Salmon library type
          description: Salmon library type
          path: workflow.data.salmon_libtype.path
          fieldType: string
          value: U
        - label: Genes expressed in minimum this many samples
          description: Genes expressed in minimum this many samples
          path: workflow.data.min_samps_gene_expr.path
          fieldType: number
          value: 3
        - label: Transcripts expressed in minimum this many samples
          description: Transcripts expressed in minimum this many samples
          path: workflow.data.min_samps_feature_expr.path
          fieldType: number
          value: 1
        - label: Minimum gene counts
          description: Minimum gene counts
          path: workflow.data.min_gene_expr.path
          fieldType: number
          value: 10
        - label: Minimum transcript counts
          description: Minimum transcript counts
          path: workflow.data.min_feature_expr.path
          fieldType: number
          value: 3
        - label: Threads
          description: Threads
          path: workflow.data.threads.path
          fieldType: number
          value: 50
workflow:
  data:
    transcriptome:
      class: File
      path: ''
    annotation:
      class: File
      path: ''
    KEYS_control_samples:
    - C4.p4
    - C5.p5
    - C6.p6
    control_samples:
    - class: File
      path: ''
    - class: File
      path: ''
    - class: File
      path: ''
    KEYS_treated_samples:
    - IR4.p4
    - IR5.p5
    - IR6.p6
    treated_samples:
    - class: File
      path: ''
    - class: File
      path: ''
    - class: File
      path: ''
    minimap_index_opts: ''
    minimap2_opts: ''
    maximum_secondary: 100
    salmon_libtype: U
    min_samps_gene_expr: 3
    min_samps_feature_expr: 1
    min_gene_expr: 10
    min_feature_expr: 3
    threads: 50
  steps:
  - Process:
      name: ''
      HostSNK:
        target: all
        cores: 5
        location:
          class: Directory
          path: .
        config_template:
          class: File
          path: config.yml
        inputs:
        - path: data.transcriptome
          confpath: transcriptome
          remap: paths
        - path: data.annotation
          confpath: annotation
          remap: paths
        - path: data.control_samples
          confpath: control_samples
          names: data.KEYS_control_samples
          remap: samples
        - path: data.treated_samples
          confpath: treated_samples
          names: data.KEYS_treated_samples
          remap: samples
        - path: data.minimap_index_opts
          confpath: minimap_index_opts
        - path: data.minimap2_opts
          confpath: minimap2_opts
        - path: data.maximum_secondary
          confpath: maximum_secondary
        - path: data.salmon_libtype
          confpath: salmon_libtype
        - path: data.min_samps_gene_expr
          confpath: min_samps_gene_expr
        - path: data.min_samps_feature_expr
          confpath: min_samps_feature_expr
        - path: data.min_gene_expr
          confpath: min_gene_expr
        - path: data.min_feature_expr
          confpath: min_feature_expr
        - path: data.threads
          confpath: threads