> For the complete documentation index, see [llms.txt](https://help.bioinsight.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.bioinsight.illumina.com/connected-insights/configure/configuration/c-pipeline-and-qc-configuration/pipeline-and-qc-yaml-reference/sample-custom-pipeline.md).

# Sample Custom Pipeline YAML

```
## Sample custom pipeline + QC configuration for Illumina Connected Insights v5.5.
##
## Download the template from Connected Insights (Configuration > General > Pipeline & QC Configuration
## > + New > "attached template"), edit the values for your own pipeline, then upload it
## to register a new pipeline together with its QC thresholds.
##
## The file has three parts:
##   1. pipeline:   registration metadata for the pipeline.
##   2. file-layout sections (sampleSheet / jointFiles / sampleFiles) describing where
##      each analysis output file is located. jointFiles is required to import variants;
##      sampleSheet and sampleFiles are optional. Stored as-is.
##   3. threshold:  the QC metrics used to build the pipeline's QC thresholds.
##
## Path placeholders such as {sampleId.DNA}, {sampleId.RNA} and {prefix} are resolved
## per case at ingestion time. A trailing ", Optional" marks a file that may be absent.

pipeline:
  # required - human-readable name shown in Connected Insights (use a report-friendly name)
  displayName: Sample Custom Pipeline v1.0.0
  # required - internal pipeline name (alphanumeric, underscore, dash only)
  name: Sample_Custom_Pipeline
  # required - pipeline version
  version: 1.0.0
  # optional - Platform Core pipeline id and urn. Provide BOTH to link the pipeline
  # to Platform Core for cloud import. Omit BOTH when Platform Core linking is not
  # needed. Either way, the pipeline supports Data Uploader and manual local upload.
  # Supplying only one is a validation error.
  icaPipelineId: 00000000-0000-0000-0000-000000000000
  icaUrn: urn:ilmn:ica:pipeline:00000000-0000-0000-0000-000000000000
  # optional - only "WGS" is meaningful here: it selects the DRAGEN-style .csv QC parser.
  # Omit this field for a TSO 500-style MetricsOutput.tsv. Any other value is treated as TSO 500 style.
  type: WGS
  # optional - glob pattern(s) whose presence signals a completed run.
  # NOTE: successMarkerFile / failureMarkerFile are used ONLY by the Connected Insights Data Uploader
  # when it monitors a local folder for auto-upload. They are ignored for Platform Core
  # cloud analysis, which reports completion via the platform's own status events.
  successMarkerFile:
    - "{prefix}/{prefix}.time_metrics.csv, Optional"
    - "{sampleId.DNA}/{sampleId.DNA}.time_metrics.csv, Optional"
    - "{sampleId.RNA}/{sampleId.RNA}.time_metrics.csv, Optional"
  # optional - file name whose presence signals a failed run (Data Uploader only)
  failureMarkerFile: "failure.txt"

## ── File-layout sections ─────────────────────────────────────────────────────────
## These describe where the analysis outputs are located and are stored verbatim.
## jointFiles is required in practice: it declares the variant files (SNV/CNV/SV/fusion),
## and an analysis imported without it brings in no variants and may fail.
## sampleSheet and sampleFiles are optional. Each file slot accepts an ordered list of
## candidate glob patterns; Connected Insights ingests the first pattern that matches.
sampleSheet:
  filePath: SampleSheet.csv
  columnAliases:
    sampleType: Sample_Type
    sampleId: Sample_ID
    pairId: PairID
  dataHeaderRowMarker:
    - "[Sample_Data]"
    - "[Cloud_Sample_Data]"

jointFiles:
  snvFiles:
    - "{sampleId.DNA}/{sampleId.DNA}.hard-filtered.vcf.gz, Optional"
    - "{prefix}/{prefix}.hard-filtered.vcf.gz, Optional"
  cnvFiles:
    - "{sampleId.DNA}/{sampleId.DNA}.cnv.vcf.gz, Optional"
    - "{prefix}/{prefix}.cnv.vcf.gz, Optional"
  svFiles:
    - "{sampleId.DNA}/{sampleId.DNA}.sv.vcf.gz, Optional"
    - "{prefix}/{prefix}.sv.vcf.gz, Optional"
  rnaFusionFiles:
    - "{sampleId.RNA}/{sampleId.RNA}.fusion_candidates.vcf.gz, Optional"
    - "{prefix}/{prefix}.fusion_candidates.vcf.gz, Optional"
  metricsQCFile:
    - "{sampleId.DNA}/{sampleId.DNA}.mapping_metrics.csv, Optional"
    - "{sampleId.DNA}/{sampleId.DNA}.wgs_coverage_metrics.csv, Optional"
    - "{sampleId.DNA}/{sampleId.DNA}.vc_metrics.csv, Optional"
    - "{sampleId.RNA}/{sampleId.RNA}.mapping_metrics.csv, Optional"
    - "{prefix}/{prefix}.mapping_metrics.csv, Optional"
    - "{prefix}/{prefix}.wgs_coverage_metrics.csv, Optional"

sampleFiles:
  tumorPairId:
    visualizationFiles:
      coverageBedFiles:
        - "{sampleId.DNA}/{sampleId.DNA}.target_bed_read_cov_report.bed, Optional"
        - "{prefix}/{prefix}.target_bed_read_cov_report.bed, Optional"
      coverageFiles:
        - "{sampleId.DNA}/{sampleId.DNA}.target.counts.gc-corrected.gz, Optional"
        - "{prefix}/{prefix}.target.counts.gc-corrected.gz, Optional"
    alignmentFiles:
      dnaBamFile:
        - "{sampleId.DNA}/{sampleId.DNA}_tumor.bam, Optional"
        - "{sampleId.DNA}/{sampleId.DNA}_tumor.cram, Optional"
        - "{prefix}/{prefix}_tumor.bam, Optional"
      dnaBaiFile:
        - "{sampleId.DNA}/{sampleId.DNA}_tumor.bam.bai, Optional"
        - "{sampleId.DNA}/{sampleId.DNA}_tumor.cram.crai, Optional"
        - "{prefix}/{prefix}_tumor.bam.bai, Optional"
      rnaBamFile:
        - "{sampleId.RNA}/{sampleId.RNA}.bam, Optional"
        - "{prefix}/{prefix}.bam, Optional"
      rnaBaiFile:
        - "{sampleId.RNA}/{sampleId.RNA}.bam.bai, Optional"
        - "{prefix}/{prefix}.bam.bai, Optional"

## ── Threshold / QC metrics ───────────────────────────────────────────────────────
## At least one metric is required. Each entry describes one QC metric completely:
##   - name:       the display label for the metric.
##   - group:      display section/group shown in Lab QC and Results.
##   - raw:        maps to the source metric. Default when display and source
##                 sections match:
##                   group: "Sample Metrics"
##                   raw: "PERCENT_Q30"
##                 Omit `raw` when display `name` equals the source metric name.
##                 Optional nested form when UI `group` should differ from the
##                 metrics-file section, or to disambiguate duplicate metric names:
##                   raw:
##                     name:  lab/DRAGEN metric name
##                     group: source section in the metrics file
##   - category:   overrides defaultCategory for this metric (RUN_QC | SAMPLE_QC | GENE_QC).
##   - type:       RANGE | BOOLEAN (RANGE covers numeric, percentage and count metrics).
##   - isLowerEnable / isUpperEnable: which bound(s) are evaluated.
##   - lowerValue / upperValue:       the bound value(s), as strings.
##   - displayInOverView:             up-level this metric to the case Results tab and report.
threshold:
  defaultCategory: SAMPLE_QC
  metrics:
    # Display name differs from the lab metric name -> map it with the raw string shorthand.
    - name: "Total Reads (Count)"
      group: "MAPPING/ALIGNING SUMMARY"
      raw: "Total input reads"
      displayInOverView: true
      type: RANGE
      isLowerEnable: true
      isUpperEnable: false
      lowerValue: "1000000"
    - name: "Estimated Sample Contamination"
      group: "MAPPING/ALIGNING SUMMARY"
      raw: "Estimated sample contamination"
      displayInOverView: true
      type: RANGE
      isLowerEnable: false
      isUpperEnable: true
      upperValue: "0.05"
    # Display name and lab name already match, so raw can be omitted entirely.
    - name: "Average alignment coverage over target region"
      group: "COVERAGE SUMMARY"
      displayInOverView: true
      type: RANGE
      isLowerEnable: true
      isUpperEnable: false
      lowerValue: "100"
    # Same metric shown under two display groups; raw.group disambiguates the source
    # group each one pulls from (tumor vs normal).
    - name: "Q30 Bases (Percentage)"
      group: "TUMOR MAPPING/ALIGNING SUMMARY (TUMOR-NORMAL)"
      raw:
        name: "Q30 bases (Percentage)"
        group: "TUMOR MAPPING/ALIGNING SUMMARY"
      type: RANGE
      isLowerEnable: true
      isUpperEnable: false
      lowerValue: "80"
    - name: "Q30 Bases (Percentage)"
      group: "NORMAL MAPPING/ALIGNING SUMMARY (TUMOR-NORMAL)"
      raw:
        name: "Q30 bases (Percentage)"
        group: "NORMAL MAPPING/ALIGNING SUMMARY"
      type: RANGE
      isLowerEnable: true
      isUpperEnable: false
      lowerValue: "80"
    # GENE_QC "Gene Coverage" metric. Its lowerValue sets the reference line on the
    # per-gene coverage plot in Results page.
    - name: "Gene Coverage"
      group: "Coverage Plot"
      category: GENE_QC
      raw: "GENE_COVERAGE"
      type: RANGE
      isLowerEnable: true
      isUpperEnable: false
      lowerValue: "900"
      disableDisplayInOverView: true
```

For field-by-field documentation, refer to [Pipeline and QC Configuration YAML](/connected-insights/configure/configuration/c-pipeline-and-qc-configuration/pipeline-and-qc-yaml-reference.md).


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