nextflow-io / nextflow-io/nextflow
nextflow clone from Gitlab does not work with non main branch or non main.nf pipeline file
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Description
Bug report
Expected behavior and actual behavior
When using nextflow clone command with a public gitlab repository, the repository should be cloned into the local folder.
Also if I provide the info for the branch and the mainScript (different from the default), then it should be used.
An error occurs. Either the project name is invalid or it is not detecting a main.nf file.
Steps to reproduce the problem
Build image with Dockerfile:
FROM quay.io/podman/stable:v4.3
RUN dnf install -y \
java-11-openjdk.x86_64 \
which \
&& dnf clean all
RUN echo "unqualified-search-registries = ['docker.io']" >> /etc/containers/registries.conf
WORKDIR /usr/bin
RUN curl -s https://get.nextflow.io | bash
and run it in podman:
podman run -it --rm registry.gitlab.com/infai/ontoflow/ontoflow-podman:main /bin/bash
In there run
nextflow -c <(printf "mainScript = test.nf") clone -r add_ci https://gitlab.com/infai/semantic-nextflow/modules
Program output
Not a valid project name: infai/semantic-nextflow/modules
Environment
- Nextflow version: 22.10.6.5843
- Java version: openjdk 11.0.18 2023-01-17
- Operating system: Linux, quay.io/podman/stable:v4.3 image in podman
- Bash version: GNU bash, version 5.2.15(1)-release (x86_64-redhat-linux-gnu)
Additional context
With (parameters at the end and an additional literal at the end)
nextflow -c <(printf "mainScript = test.nf") clone https://gitlab.com/infai/semantic-nextflow/modules -r add_ci page
the error is:
Remote resource not found: https://gitlab.com/api/v4/projects/infai%2Fsemantic-nextflow%2Fmodules/repository/files/main.nf?ref=main
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
Reproduce the reported nextflow clone commands in the provided Podman/Docker environment, using the GitLab repository, add_ci branch, and test.nf script. Trace the clone handling for GitLab URLs, branch selection, and non-default main scripts; done means the repository clones successfully without requiring main.nf or the default branch.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- docker, gitlab, java
- Domain
- cli
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100