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RIDE Configuration Files

This directory contains all configuration files required to run the RIDE pipeline. Each run uses these files to define samples, input data, reference resources, and analysis parameters.

The full config/ directory is copied into each run folder to guarantee complete reproducibility.

1. Main configuration file: config.yaml

The main configuration file defines input tables, reference resources, and tool-specific parameters.

Input tables

samples: config/samples.tsv
units: config/units.tsv
reheader: config/reheader.tsv
  • samples.tsv: defines biological samples and their associated sequencing units
  • units.tsv: defines FASTQ files for each sequencing unit
  • reheader.tsv: optional mapping between internal sample IDs and human-readable names

Reference resources

Genome reference

resources:
  genome:
    basepath: "/path/to/refdata"
    provider: "ensembl"
    release: "GRCh38"
    fasta: "Homo_sapiens.GRCh38.dna.primary_assembly.fa"
    gtf: "Homo_sapiens.GRCh38.115.gtf"
  • basepath: directory containing reference files
  • fasta: genome FASTA file
  • gtf: gene annotation file (GTF format)

Transcriptome reference (kallisto)

transcriptome:
  basepath: "/path/to/refdata"
  provider: "ensembl"
  release: "GRCh38"
  cdna: "Homo_sapiens.GRCh38.cdna.all.fa.gz"

Used to build the kallisto index.

RSeQC resources

rseqc:
  basepath: "/path/to/refdata"
  provider: "rseqc"
  release: "hg38"
  housekeeping: "hg38.HouseKeepingGenes.bed"
  refseq: "hg38_RefSeq.bed"

Used for RNA-seq quality control metrics.

Trimming parameters

trimming:
  quality: 20
  min_length: 20
  trim_poly_g: true
  trim_poly_x: true
  detect_adapter: true

Defines read trimming and adapter detection settings.

Kallisto parameters

kallisto:
  index_name: "kallisto_index.idx"
  frag_len: 280
  frag_sd: 80
  boot: 100
  • frag_len, frag_sd: fragment length parameters (single-end data)
  • boot: number of bootstrap samples

STAR parameters

star:
  index_dir: "index"
  sjdb_overhang: 100
  • index_dir: STAR genome index directory
  • sjdb_overhang: read length minus one

2. Sample definition: samples.tsv

Defines biological samples and their associated sequencing units.

sample	units
ERS179576	HSQ1008_141.L005.ERS179576,HSQ1008_141.L007.ERS179576,HSQ1009_88.L001.ERS179576
ERS179577	HSQ1009_86.L001.ERS179577
  • sample: unique biological sample identifier
  • units: comma-separated list of sequencing units belonging to the sample

3. Sequencing units: units.tsv

Defines FASTQ files associated with each sequencing unit.

sample	unit	fq1	fq2
ERS179576	HSQ1008_141.L005.ERS179576	path_to_datasets/ERR174310_1.fastq.gz	path_to_datasets/ERR174310_2.fastq.gz
ERS179576	HSQ1008_141.L007.ERS179576	path_to_datasets/ERR174312_1.fastq.gz	path_to_datasets/ERR174312_2.fastq.gz
ERS179576	HSQ1009_88.L001.ERS179576	path_to_datasets/ERR174314_1.fastq.gz
ERS179577	HSQ1009_86.L001.ERS179577	path_to_datasets/ERR174324_1.fastq.gz	path_to_datasets/ERR174324_2.fastq.gz
  • sample: biological sample ID (must match samples.tsv)
  • unit: sequencing unit / lane / library identifier
  • fq1: FASTQ file (read 1)
  • fq2: FASTQ file (read 2, optional for single-end data)

4. Sample renaming: reheader.tsv

Optional mapping from internal sample IDs to human-readable names used in reports and plots.

sample_id	sample_name
ERS179576	76
ERS179577	77
  • sample_id: original sample identifier
  • sample_name: label used in downstream outputs

Notes

  • All paths can be absolute or relative
  • Samples with missing FASTQ files will cause the pipeline to fail
  • The configuration directory is copied into each run directory to ensure full traceability