nextflow-io/nextflow

A flag to remove quotation marks from index file

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#5,546 opened on Nov 27, 2024

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 (2 comments) (0 reactions) (0 assignees)Groovy (784 forks)batch import
good first issuestale

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Description

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

Contributor guide

Research direction
Locate the index file generation code in Nextflow's source (likely in the workflow or execution layer) where values are quoted. Propose adding a flag (e.g., ` no quote index`) that suppresses quotation marks and ensure the `.splitCsv` operator can directly read unquoted values.
Tech stack
groovy
Domain
backendcli
Issue type
Feature
DifficultyEstimated implementation difficulty for a new contributor, from 1 for very small changes to 5 for expert-level work.
2
Estimated timeA rough time range for an experienced contributor to investigate, implement, test, and prepare a pull request.
1-3 hours
Activity statusHow available the issue appears right now: fresh, active, stale, blocked, or waiting on maintainer input.
Needs maintainer response
ClarityHow clearly the issue explains the expected change, acceptance criteria, and next step.
Clear
Prerequisites
GitNextflow
Newbie friendlinessA 1-100 score estimating how approachable this issue is for first-time contributors.
60