Description of the bug
Consider: a clean fork of nf-core/modules at https://github.com/organization/nf-core-modules.git, where the org is configured as my-organization. Feature branch feature/my-workflow provides the following:
- subworkflow my-organization/my_subworkflow
- component: module my-organization/mymodule/command1
- component: module nf-core/fastqc
Running the command to update the subworkflow from this branch, and accepting the option to update all modules, causes a crash on updating fastqc. The root cause is that it tries to find branch feature/my-workflow on repo https://github.com/nf-core/modules.git, which does not exist.
Unable to provide actual terminal output due to my company's policy.
Command used and terminal output
$ nf-core subworkflows --git-remote https://github.com/organization/nf-core-modules.git --branch feature/my-workflow update my_subworkflow
System information
Python 3.12.8, Rocky Linux 9 on AWS, nf-core tools v4.0.2; nextflow version not applicable
Description of the bug
Consider: a clean fork of
nf-core/modulesathttps://github.com/organization/nf-core-modules.git, where the org is configured asmy-organization. Feature branchfeature/my-workflowprovides the following:Running the command to update the subworkflow from this branch, and accepting the option to update all modules, causes a crash on updating fastqc. The root cause is that it tries to find branch
feature/my-workflowon repohttps://github.com/nf-core/modules.git, which does not exist.Unable to provide actual terminal output due to my company's policy.
Command used and terminal output
$ nf-core subworkflows --git-remote https://github.com/organization/nf-core-modules.git --branch feature/my-workflow update my_subworkflowSystem information
Python 3.12.8, Rocky Linux 9 on AWS, nf-core tools v4.0.2; nextflow version not applicable