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create nf-co sample sheet

createNfCorePipelineSampleSheet.Rd

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)