My pipeline uses a sample file that stores relative paths to resource files. Running the pipeline with nextflow itself works fine, but with nf-test, it can’t find the resource files. I have tried a few things that did not work:
- Specifying $baseDir/[relative path] in the sample file for the resource file paths
- Using stage {symlink “.”} in the nextflow_pipeline closure to try and stage the base directory (which is what the resource file paths are with respect to)
Using absolute paths to the resource files works. But this is not compatible with permitting other users to run unit tests on their machines.