Outputs¶

A run writes a reproducible output directory. By default this is encode_results/; change it with --outdir.

Directory layout¶

encode_results/
  manifest.tsv
  metadata.jsonl
  files/
    case/
      ENCSR...
        ENCFF....fastq.gz
    control/
      ENCSR...
        ENCFF....fastq.gz
  nfcore_*_samplesheet.csv
  snakemake_*_samplesheet.csv

files/ is created only when downloads are enabled. With --metadata-only, ENCODEfetch writes metadata and samplesheets without downloading files.

manifest.tsv¶

manifest.tsv is the main tidy table. It contains one row per matched file before FASTQ collapsing, or one row per pair after collapse_fastq_pairs.

Important columns include:

Column	Description
`experiment_accession`	ENCODE experiment accession.
`is_control`	`True` for matched control experiments, `False` for case experiments.
`matched_control_experiments`	Comma-separated experiment-level controls from ENCODE `possible_controls`.
`controlled_by_files`	Normalized file accessions from ENCODE file-level `controlled_by` links.
`assay_title`	ENCODE assay title.
`target_label`	Target label for ChIP-style assays.
`organism`	Donor organism scientific name.
`biosample_term_name`	Biosample ontology term name.
`file_accession`	ENCODE file accession.
`file_format`	File format such as `fastq`, `bam`, `bed`, or `bigWig`.
`output_type`	ENCODE output type.
`assembly`	Genome assembly where applicable.
`md5sum`	ENCODE file checksum.
`file_size`	File size in bytes.
`url`	Absolute ENCODE download URL.
`local_path`	Local downloaded file path, when downloads are performed.

After FASTQ collapsing, additional helper columns can include fastq_1, fastq_2, single_end, file_accession_r2, local_path_r2, and url_r2.

metadata.jsonl¶

metadata.jsonl stores one JSON object per record. It is useful for audit trails and downstream tools that prefer line-delimited JSON.

Samplesheets¶

Samplesheets are written only when requested:

--nfcore writes nfcore_*_samplesheet.csv.
--snakemake writes snakemake_*_samplesheet.csv.

Samplesheet rows prefer local downloaded paths when they are available, then fall back to remote URLs.