nextflow-io / nextflow-io/nextflow

CLI doesn't recognize local copy of project pulled from gitlab subgroups

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software/git stale
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Description

Bug report

Expected behavior and actual behavior

I wanted to do use the nextflow drop command to remove the local copy of a project after it is finished running. After running or pulling my pipeline by url from gitlab where it is located in a subgroup, the local copy of the project can be found in ~/.nextflow/assets/organization/group1/group2/project_name. I expect to be able to drop the project by referring to organization/group1/group2/project_name, but I am told it is not a valid project name. Running nextflow list outputs organization/group1 when I would expect organization/group1/group2/project_name. I tried dropping organization/group1 since it was listed, but this also fails.

Steps to reproduce the problem
nextflow pull https://gitlab.com/DPIPE/datasharing/varde/alamut-exporter -r 3-exclude-interpretations-in-db-based-on-some-parameter
nextflow drop DPIPE/datasharing/varde/alamut-exporter
nextflow list
nextflow drop DPIPE/datasharing
Program output
Checking https://gitlab.com/DPIPE/datasharing/varde/alamut-exporter ...
 downloaded from https://gitlab.com/DPIPE/datasharing/varde/alamut-exporter.git - revision: 4e9f319a7d [3-exclude-interpretations-in-db-based-on-some-parameter]
Not a valid project name: DPIPE/datasharing/varde/alamut-exporter
DPIPE/datasharing
Can't find git repository config file -- Repository may be corrupted: <HOME>/.nextflow/assets/DPIPE/datasharing
Environment
  • Nextflow version: nextflow version 23.04.4.5883
  • Java version: openjdk version "11.0.20.1" 2023-08-24
  • Operating system: Linux
  • Bash version: (use the command $SHELL --version): fish, version 3.3.1

Update: tried running the same steps with nextflow version 23.10.1 build 5891, same result

Additional context

Contributor guide

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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 by reproducing the reported commands with a GitLab project nested in subgroups: nextflow pull, nextflow drop, and nextflow list. Trace the CLI entry points for drop and list and how they resolve repositories under ~/.nextflow/assets; done means the full subgroup path is listed and can be removed successfully.

Written by the indexing model from the issue text.

Assessment

Tech stack
git
Domain
cli
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
42/100

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