createNfCorePipelineSampleSheet: create nf-co sample sheet

In cmatKhan/brentlabRnaSeqTools: A Collection of Functions to Interact with the Brentlab RNASeq Database

Description

create a samplesheet for the nf-co rnaseq pipeline https://nf-co.re/rnaseq/3.2/usage#samplesheet-input

Usage

createNfCorePipelineSampleSheet(
  metadata,
  sample_columns,
  sequence_dir_prefix,
  check_files_flag = FALSE
)

Arguments

metadata	most likely from the database. must include runNumber, fastqFileName, libraryProtocol, and the columns used to create the sample name (see param sample_columns)
sample_columns	a character vector of columns to concat into a sample identifier. eg c("genotype1", "fastqFileNumber")
sequence_dir_prefix	path to directory where the sequence run directories are stored. eg /mnt/htcf_lts/lts_sequence
check_files_flag	default FALSE. Set to true to check that files exist

Value

a dataframe with the columns which correspond to those required for the nf-co rnaseq pipeline sample sheet. See https://nf-co.re/rnaseq/3.2/usage#samplesheet-input

Note

: currently hard coded to set strandedness to 'reverse' if libraryProtocol is E7420L, or 'unstranded', AND for single strand libraries (fastq2 is an empty string)

cmatKhan/brentlabRnaSeqTools documentation built on Nov. 17, 2021, 5:47 a.m.