Configuration Reference¶

This page is an exhaustive reference for every parameter in config.yaml. The pipeline validates your config against a JSON Schema before any jobs run — so typos and missing required fields are caught early.

Run the validator manually at any time with:

pixi run lint local-references laptop

Minimal working config¶

globals:
  results_folder: results/my_analysis/

genome:
  label: mm10

comparisons:
  - name: my_experiment
    protocol: pe
    sample_sheet: samples.csv

This processes a paired-end dataset using mm10 references downloaded automatically, with all defaults applied.

`globals`¶

Key	Required	Default	Description
`results_folder`	Yes	—	Root directory where all outputs (BAMs, counts, logs) are written. Use a unique path per experiment.

`genome`¶

Controls which reference genome is used.

Automatic (Refgenie)Custom local files

Provide a label and omit fasta_path / gtf_path. References are fetched automatically.

genome:
  label: mm10

Supported labels: mm10, mm39.

Key	Required	Default	Description
`label`	Yes	—	Genome version.
`annotation_type`	No	`ensembl`	GTF format: `ensembl`, `gencode`, or `mgi`.
`selected_chromosomes`	No	all	Restrict analysis to a chromosome list. Useful for pilot runs.

Keep label and add explicit paths. fasta_path, gtf_path and annotation_type are required together. The label is still used to fetch RepeatMasker and GtRNAdb annotations.

genome:
  label: mm10
  fasta_path: /data/refs/my_genome.fa
  gtf_path: /data/refs/my_genome.gtf
  annotation_type: ensembl

Key	Required	Default	Description
`label`	Yes	—	`mm10` or `mm39`.
`fasta_path`	Yes (with gtf)	—	Absolute path to genome FASTA.
`gtf_path`	Yes (with fasta)	—	Absolute path to gene annotation GTF.
`annotation_type`	Yes (with fasta)	—	`ensembl`, `gencode`, or `mgi`.
`selected_chromosomes`	No	all	Restrict to a chromosome subset.

Warning

The validator rejects a config that sets only some of fasta_path, gtf_path and annotation_type.

`comparisons`¶

A list of independent analyses. Each entry specifies a sample sheet and its own alignment and differential expression settings. You can have multiple comparisons in one config — the pipeline runs them in parallel.

comparisons:
  - name: experiment_A
    protocol: pe
    sample_sheet: samples_A.csv
    deseq2:
      variable: genotype
      reference_level: WT
  - name: experiment_B
    protocol: se
    sample_sheet: samples_B.csv
    strandedness: 2
    deseq2:
      variable: treatment
      reference_level: control

Required keys per comparison¶

Key	Required	Description
`name`	Yes	Label for this comparison. Used to name output subdirectories.
`protocol`	For paired-end	Set `pe` for paired-end data (sample sheet columns `filename_1`/`filename_2`). Any other value, or omitting it, means single-end (`filename` column).
`sample_sheet`	Yes	Path to the CSV file (relative to `--directory`, or absolute).

DESeq2 settings¶

These can be set per-comparison, or as global defaults under defaults.deseq2. A per-comparison value always takes precedence over the global default.

Key	Default	Description
`deseq2.test`	`Wald`	Statistical test: `Wald` or `LRT`.
`deseq2.variable`	`genotype`	Sample-sheet column used to define contrast groups. Must match an existing column name.
`deseq2.reference_level`	(none)	The baseline level of `variable` (fold-change denominator). Strongly recommended — without it DESeq2 picks an arbitrary reference.

Alignment overrides¶

Key	Default	Description
`strandedness`	`0`	Library strandedness: `0` unstranded, `1` forward, `2` reverse.
`trimmomatic`	TruSeq3 defaults	Fixed Trimmomatic string, or `{adaptive: true}` for automatic parameter derivation.
`star`	`--seedSearchStartLmax 30 --outFilterMismatchNoverReadLmax 0.04 --winAnchorMultimapNmax 40`	Extra CLI flags passed to the STAR aligner.
`bamCoverage`	`--binSize 50 --normalizeUsing None`	Extra flags for `deeptools bamCoverage`.

`defaults`¶

Global fallbacks applied to every comparison when no per-comparison override is set. Useful to avoid repeating the same setting in each comparison.

defaults:
  strandedness: 2
  deseq2:
    test: Wald
    variable: genotype
    reference_level: WT

Key	Default	Description
`strandedness`	`0`	Applied to all comparisons that don't set their own `strandedness`.
`deseq2.test`	`Wald`	Default test type.
`deseq2.variable`	`genotype`	Default contrast variable.
`deseq2.reference_level`	(none)	Default reference level.

Module flags¶

Disable optional analysis modules to save computation time.

disable_TE_analysis: false        # set true to skip STAR-TE and SalmonTE
disable_salmonTE_analysis: false  # set true to skip SalmonTE only
disable_tRNA_analysis: false      # set true to skip tRNA quantification

Expert parameters¶

These settings are rarely needed. Refer to the Analysis Modules documentation for context.

STAR-TE multi-mapping modes

defaults:
  starTE_random:
    outFilterMultimapNmax: 5000    # default
    winAnchorMultimapNmax: 5000    # default
    alignTranscriptsPerWindowNmax: 300  # default
  starTE_multihit:
    outFilterMultimapNmax: 1       # default
    winAnchorMultimapNmax: 5000    # default
    alignTranscriptsPerWindowNmax: 3000 # default

Per-comparison overrides use the same keys under the comparison entry.

tRNA quantification

tRNA_quantification:
  method: standard          # or "mim-tRNA-seq"
  mimseq_params:
    max_mismatches: 2       # default
    cluster_identity: 0.8   # default
    min_cov: 10             # default

Use mim-tRNA-seq only if your libraries were prepared with the mim-tRNA-seq protocol.