Generate nf-core samplesheet manifest — generate_nfcore

Generate a samplesheet manifest for nf-core workflows (rnaseq or sarek) from Synapse dataset metadata. The function queries the dataset metadata table and reformats it into the appropriate samplesheet format where each row represents a biological sample that may have multiple associated files.

Usage

generate_nfcore_manifest(
  dataset_id,
  workflow_name,
  synstage = FALSE,
  output_file = NULL,
  strandedness = "auto"
)

Arguments

dataset_id: Synapse ID of the dataset to query
workflow_name: Name of the nf-core workflow ("rnaseq" or "sarek")
synstage: Logical indicating whether to use Synapse staging for file paths
output_file: Optional path to save the samplesheet CSV file. If NULL, returns the data frame.
strandedness: For rnaseq workflow, strandedness setting ("forward", "reverse", "unstranded", or "auto"). Defaults to "auto".

Value

A data frame with the samplesheet format appropriate for the specified workflow

Examples

if (FALSE) { # \dontrun{
# Generate rnaseq samplesheet
rnaseq_manifest <- generate_nfcore_manifest(
  dataset_id = "syn12345678",
  workflow_name = "rnaseq",
  synstage = TRUE
)

# Generate sarek samplesheet
sarek_manifest <- generate_nfcore_manifest(
  dataset_id = "syn12345678", 
  workflow_name = "sarek",
  synstage = FALSE
)
} # }