nextflow-io / nextflow-io/nextflow

`pull` and `run` treat Github usernames as case sensitive on Linux

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#5,280 4 comments 1 reaction 0 assignees View on GitHub

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software/git stale triage/investigate
Dominant language
Groovy
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Description

Bug report

Expected behavior and actual behavior

I mention both pull and run because that is how I found the bug, but I confirmed it with just pull.

Expected:
Calling nextflow pull nextflow-io/hello or nextflow pull Nextflow-io/hello should pull/update the same pipeline.

Actual:
Calling these two above commands generates two different folders in $NXF_HOME/assets:

Steps to reproduce the problem
❯ nextflow pull Nextflow-io/hello
Checking Nextflow-io/hello ...
 downloaded from https://github.com/nextflow-io/hello.git - revision: afff16a9b4 [master]

❯ nextflow pull nextflow-io/hello
Checking nextflow-io/hello ...
 downloaded from https://github.com/nextflow-io/hello.git - revision: afff16a9b4 [master]

❯ ls $NXF_HOME/assets/
nextflow-io/ Nextflow-io/

Environment
  • Nextflow version: 24.04.4 build 5917
  • Java version: OpenJDK 64-Bit Server VM 11.0.22+7-LTS
  • Operating system: Red Hat Enterprise Linux 9.3 (Plow) Linux 5.14.0-362.24.1.el9_3.x86_64
  • Bash version: GNU bash, version 5.1.8(1)-release (x86_64-redhat-linux-gnu)
Additional context

Slack discussion

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the command entry points for nextflow pull and nextflow run, then trace how the GitHub owner and repository become the $NXF_HOME/assets path. Reproduce the two commands from the report and verify that differently cased usernames resolve to one shared pipeline directory.

Written by the indexing model from the issue text.

Assessment

Tech stack
groovy
Domain
cli
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
45/100

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