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I want to run pipeline from github, which is in a repository and is within a subfolder.
and when i run the following command to run the pipeline nextflow run https://github.com/franci-r/CELLO_pipeline -main-script /CCB/step_2.nf -r main 23:48
the pipeline works but it NEEDS a main.nf file in the root directory of the git, even if the main file... is empty
This discussion was converted from issue #5873 on March 11, 2025 10:12.
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I want to run pipeline from github, which is in a repository and is within a subfolder.
and when i run the following command to run the pipeline nextflow run https://github.com/franci-r/CELLO_pipeline -main-script /CCB/step_2.nf -r main
23:48
the pipeline works but it NEEDS a main.nf file in the root directory of the git, even if the main file... is empty
the code that is run is acc in the sub directory I instruct it to use. But if i remove the main.nf file it says: Pulling franci-r/CELLO_pipeline ...
WARN: Cannot read project manifest -- Cause: Remote resource not found: https://api.github.com/repos/franci-r/CELLO_pipeline/contents/nextflow.config?ref=master
Remote resource not found: https://api.github.com/repos/franci-r/CELLO_pipeline/contents/main.nf?ref=master
Is this my mistake, or?
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