csv as input

[lmfaber]

csv as input

[hoelzer]

Ah ok, I think now I understand what you meant in #8. But still, in a normal use case people will have either single-end or paired-end reads and assemble the set with different tools. So the input should be not single- and paired-end reads at one time. Allowing both types as a mixed input complicates everything I guess.

Here some example code for CSV input that might help as a starting point:

// illumina reads input & --list support
if (params.illumina && params.list) { illumina_input_ch = Channel
  .fromPath( params.illumina, checkIfExists: true )
  .splitCsv()
  .map { row -> ["${row[0]}", [file("${row[1]}", checkIfExists: true), file("${row[2]}", checkIfExists: true)]] }
  .view() }
else if (params.illumina) { illumina_input_ch = Channel
  .fromFilePairs( params.illumina , checkIfExists: true )
  .view() }

In this case, FASTQ files are provided to the params.illumina parameter and if additionally params.list == true a CSV is expected instead of the FASTQs directly.