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Metadata for processed products

Source: R/nextflow_annotation_utils.R
processed_meta.Rd

Wrapper for all steps to get manifest for processed product

Usage

processed_meta(
  input,
  output,
  workflow_link,
  use_sample_as_specimen_id = FALSE,
  publish_dir = NULL
)

Arguments

input

Data from map_sample_input_ss.

output

Data from map_sample_output_*.

Workflow link.

use_sample_as_specimen_id

If TRUE, sets specimenID from the sample column (parsed from directory structure/filenames) instead of inheriting from input files.

publish_dir

Top-level publish directory for finding workflow assets like SAMtools stats.

Value

List manifest with manifests for each processed dataset, and sample_io with linked inputs and outputs (should be used for provenance annotation).