nextflow-io / nextflow-io/nextflow
CLI doesn't recognize local copy of project pulled from gitlab subgroups
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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
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- 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