nextflow-io/nextflow

A flag to remove quotation marks from index file

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#5,546 建立於 2024年11月27日

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 (1 留言) (0 反應) (0 負責人)Groovy (3,382 star) (784 fork)batch import
good first issuestale

描述

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

貢獻者指南

技術棧
groovy
領域
clideveloper experience
議題類型
feature
難度面向新貢獻者的預計實作難度，1 表示很小改動，5 表示專家級工作。
3
預計時間有經驗貢獻者完成調查、實作、測試並準備 pull request 的粗略時間範圍。
1-3 hours
活動狀態議題目前的可參與程度：新鮮、活躍、陳舊、阻塞或等待維護者輸入。
fresh
清晰度議題是否清楚說明預期改動、驗收標準和下一步。
clear
前置要求
Familiarity with Nextflow internalsGroovy programming
新手友善度1-100 的估計分數，表示該議題對首次貢獻者的友善程度。
60
研究方向
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.