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

harper357 commented 1 month ago

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 commented 1 month ago

@ewels

pditommaso commented 1 month ago

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 commented 1 month ago

Yup, so taking the first example:

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

Nextflow looks for Nextflow-io/hello
Nextflow finds https://github.com/nextflow-io/hello.git
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.

nextflow-io / nextflow