A flag to remove quotation marks from index file

New feature

Usage scenario

I want to create a several entry point for the pipeline, so that users would be able to rerun my pipeline from the middle. This requires a creation of file list which are required to run pipeline from middle entry point (see example).

Suggest implementation

For this I find index file creation a very useful feature. The only problem is that quotation marks are added to the values. This makes index files more difficult to read as well as prevents a direct reading from them with .splitCsv operator as quotation marks are still left. This causes an error:

ERROR ~ Error executing process > 'PYCISTOPIC:INFERPEAKS:InferConsensus (22)'
Caused by:
  Not a valid path value: '"home/launchdir/results/narrowPeaks/neurons_peaks.narrowPeak"'

So it would be great to have a way to remove quotation marks from index file

Start with the index-file creation behavior described in the issue and compare it with the linked Nextflow index-files documentation; then trace how the resulting file is consumed by splitCsv. Done means an opt-in flag produces an index file without quotation marks and the generated file can be read without the quoted-path error.