nextflow-io/nextflow
A flag to remove quotation marks from index file
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#5546 aperta il 27 nov 2024
good first issuestale
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Descrizione
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