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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 (1 comment) (0 reactions) (0 assignees)Groovy (3,382 stars) (784 forks)batch import
good first issuestale

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

Tech stack
groovy
Domain
clideveloper experience
Issue type
feature
DifficultyEstimated implementation difficulty for a new contributor, from 1 for very small changes to 5 for expert-level work.
3
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.
fresh
ClarityHow clearly the issue explains the expected change, acceptance criteria, and next step.
clear
Prerequisites
Familiarity with Nextflow internalsGroovy programming
Newbie friendlinessA 1-100 score estimating how approachable this issue is for first-time contributors.
60
Research direction
The issue requests a flag to remove quotation marks from index files generated by Nextflow. Start by examining the index file writing logic in the Nextflow codebase, likely around the `IndexFile` class or related pipeline components. Look for where quotation marks are added to file paths and consider adding a configuration option (e.g., `quoteIndexValues`) that defaults to `true` for backward compatibility.