Skip to contents

Map sample to output from nf-rnaseq with path

Source: R/nextflow_annotation_utils.R
map_sample_output_rnaseq.Rd

See https://nf-co.re/rnaseq/docs/output/#pipeline-overview. The workflow generates several types of outputs that can become ("level 2" or "level 3") dataset products. (note: some outputs may not be available depending on how workflow was run and indexed back).

Usage

map_sample_output_rnaseq(
  syn_out,
  fileview,
  output = c("STAR and Salmon", "featureCounts", "SAMtools")
)

Arguments

syn_out

Syn id of variant calling output folder.

fileview

An existing fileview to use (usually the project's local fileview) that scopes outputs and has "default" columns (id, name, type, parentId, path, ...). See details.

output

Which output to select and annotate. Defaults to all output types unless more limited election.

  • "STAR and Salmon" selects .sf files – this is typically considered the main output.

  • "featureCounts" selects the relevant .txt files.

  • "SAMtools" selects the .bam/.bai indexed and sorted by SAMtools.

Value

A list of data.tables with columns output_name output_id sample workflow for each output type. An attribute workflow=nf-rnaseq will be set on the returned list, and elements will have attribute outputFrom set, e.g. outputFrom=SAMtools.