nextflow-io/nextflow

A flag to remove quotation marks from index file

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#5,546 opened on 2024年11月27日

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

説明

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

コントリビューターガイド

技術スタック
groovy
領域
clideveloper experience
Issue 種別
feature
難度新しい貢献者にとっての実装難度です。1 は非常に小さな変更、5 は専門的な作業です。
3
推定時間経験ある貢献者が調査、実装、テスト、pull request 準備にかけるおおよその時間範囲です。
1-3 hours
活動状況Issue が今どれだけ取り組みやすいかを示します。新しい、活発、古い、ブロック中、またはメンテナー入力待ちなどです。
fresh
明確さ期待される変更、受け入れ条件、次の手順がどれだけ明確かを示します。
clear
前提条件
Familiarity with Nextflow internalsGroovy programming
初心者向け度初回貢献者にどれだけ取り組みやすいかを 1-100 で推定したスコアです。
60
調査方針
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.