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

[harper357]

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

[harper357]

@ewels

[pditommaso]

What it could be investigate if there's a way to use the GitHub URI as source of truth to name to local path.

[ewels]

Yup, so taking the first example:

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

1. Nextflow looks for Nextflow-io/hello
2. Nextflow finds https://github.com/nextflow-io/hello.git
3. Nextflow creates the assets directory based on the remote name + capitlisation: nextflow-io/hello

This way there will only ever be one capitalisation possible for assets on any given pipeline.

[stale]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.