name: sarek
version: "3.7.1"
description: "Variant calling for WGS/WES data (germline and somatic)"

# Documentation and source - NOTE: Update version in URLs when upgrading pipeline
urls:
  documentation: "https://nf-co.re/sarek/{version}/"
  parameters: "https://nf-co.re/sarek/{version}/parameters/"
  output_docs: "https://nf-co.re/sarek/{version}/docs/output/"
  github: "https://github.com/nf-core/sarek"
  releases: "https://github.com/nf-core/sarek/releases"

data_types:
  - WGS
  - WES
  - whole genome sequencing
  - whole exome sequencing
  - tumor-normal
  - germline
  - somatic

detection_hints:
  filename:
    - tumor
    - normal
    - germline
    - wgs
    - wes
    - exome
    - dna
    - variant
  directory:
    - variant
    - wgs
    - wes
    - exome
    - germline
    - somatic

samplesheet:
  input_types:
    - fastq
    - bam
    - cram

  columns:
    - name: patient
      required: true
      type: string
      inference: filename
      description: "Patient/subject identifier for grouping samples"

    - name: sample
      required: true
      type: string
      inference: filename
      description: "Sample identifier (e.g., tumor, normal)"

    - name: lane
      required: false
      type: string
      default: "L001"
      inference: filename
      description: "Sequencing lane"

    - name: fastq_1
      required: true
      type: path
      inference: auto
      condition: "input_type == 'fastq'"
      description: "Absolute path to R1 FASTQ"

    - name: fastq_2
      required: false
      type: path
      inference: auto
      condition: "input_type == 'fastq'"
      description: "Absolute path to R2 FASTQ"

    - name: bam
      required: true
      type: path
      inference: auto
      condition: "input_type in ['bam', 'cram']"
      description: "Absolute path to BAM/CRAM file"

    - name: bai
      required: true
      type: path
      inference: auto
      condition: "input_type in ['bam', 'cram']"
      description: "Absolute path to BAM/CRAM index"

    - name: status
      required: false
      type: integer
      allowed:
        - 0
        - 1
      default: 0
      inference: filename
      description: "0=normal, 1=tumor (critical for somatic calling)"

decision_points:
  - parameter: genome
    prompt: "Which reference genome should be used?"
    options:
      - value: GRCh38
        label: "Human GRCh38/hg38 (recommended)"
        description: "Latest human reference with most annotation support"
      - value: GRCh37
        label: "Human GRCh37/hg19 (legacy)"
        description: "For compatibility with older datasets"
      - value: mm10
        label: "Mouse mm10"
        description: "Mouse reference genome"
    default: GRCh38
    recommendation: "Default to GRCh38 for human data"

  - parameter: tools
    prompt: "What type of variant calling do you need?"
    options:
      - value: "haplotypecaller,snpeff"
        label: "Germline variants (single samples)"
        description: "For finding inherited variants in normal samples"
        condition: "no tumor samples detected"
      - value: "mutect2,strelka,snpeff"
        label: "Somatic variants (tumor-normal pairs)"
        description: "For finding cancer mutations with matched normal"
        condition: "tumor-normal pairs detected"
      - value: "haplotypecaller,deepvariant,snpeff"
        label: "Germline with DeepVariant"
        description: "Higher accuracy germline calling (requires GPU)"
      - value: "mutect2,manta,snpeff"
        label: "Somatic with structural variants"
        description: "Comprehensive tumor analysis including SVs"
    default: "haplotypecaller,snpeff"
    recommendation: "Use somatic tools if tumor/normal pairs detected, otherwise germline"

  - parameter: wes
    prompt: "Is this whole exome sequencing (WES) data?"
    options:
      - value: "false"
        label: "No - Whole Genome Sequencing (WGS)"
        description: "Full genome coverage"
      - value: "true"
        label: "Yes - Whole Exome Sequencing (WES)"
        description: "Requires --intervals BED file"
    default: "false"
    recommendation: "If WES, user must provide intervals BED file"

test_profile:
  command: "nextflow run nf-core/sarek -r 3.7.1 -profile test,docker --outdir test_sarek"
  duration: "20 minutes"
  success_indicators:
    - "test_sarek/multiqc/multiqc_report.html"
  log_pattern: "Pipeline completed successfully"

run_command:
  template: |
    nextflow run nf-core/sarek \
        -r 3.7.1 \
        -profile docker \
        --input {samplesheet} \
        --outdir {outdir} \
        --genome {genome} \
        --tools {tools} \
        -resume

  wes_template: |
    nextflow run nf-core/sarek \
        -r 3.7.1 \
        -profile docker \
        --input {samplesheet} \
        --outdir {outdir} \
        --genome {genome} \
        --tools {tools} \
        --wes \
        --intervals {intervals} \
        -resume

outputs:
  primary:
    - path: "preprocessing/recalibrated/*.recal.bam"
      description: "Analysis-ready BAM files"
    - path: "variant_calling/*/*.vcf.gz"
      description: "Variant call files"
    - path: "annotation/snpeff/*.ann.vcf.gz"
      description: "Annotated variants"

  validation:
    - file: "multiqc/multiqc_report.html"
      check: exists
      description: "QC report must exist"
    - file: "preprocessing/recalibrated"
      check: exists
      description: "Recalibrated BAMs directory"

resources:
  min_memory: "16.GB"
  recommended_memory: "64.GB"
  wgs_memory: "128.GB"
  min_cpus: 4
  recommended_cpus: 16
  disk_space: "500.GB"

troubleshooting:
  - error: "BQSR fails"
    fix: "Check known sites available for genome. Skip with --skip_bqsr for non-standard references"
  - error: "Mutect2 no variants"
    fix: "Verify tumor/normal pairing in samplesheet (check status column: 0=normal, 1=tumor)"
  - error: "Out of memory"
    fix: "--max_memory '128.GB' for WGS data"
  - error: "DeepVariant GPU issues"
    fix: "Ensure NVIDIA Docker runtime configured, or use CPU mode"

tumor_normal_keywords:
  tumor:
    - tumor
    - tumour
    - met
    - metastasis
    - primary
    - cancer
    - malignant
  normal:
    - normal
    - germline
    - blood
    - pbmc
    - control
    - healthy
    - matched