Description of feature
When using nf-core pipelines download with the test datasets, which refers to online resources, the run is not locally executable. Pulling referenced URLs would be a useful feature for test runs.
I have written a small script that does exactly that. It takes a resolved config from nextflow config -flat "${config_path}" -profile "${test_profile}" > "${resolved_config_path}" and pulls referenced http(s) protocol files. It's still pretty simple, but it looks up dependencies recursively and replaces their references with local pulls.
What is currently not in scope of the script:
- Pulling S3 buckets and other protocols
- Filtering out resources that don't need pulling e.g. project websites
fetch.py
Would this be a desired feature for nf-core/tools?
Description of feature
When using
nf-core pipelines downloadwith the test datasets, which refers to online resources, the run is not locally executable. Pulling referenced URLs would be a useful feature for test runs.I have written a small script that does exactly that. It takes a resolved config from
nextflow config -flat "${config_path}" -profile "${test_profile}" > "${resolved_config_path}"and pulls referenced http(s) protocol files. It's still pretty simple, but it looks up dependencies recursively and replaces their references with local pulls.What is currently not in scope of the script:
fetch.py
Would this be a desired feature for
nf-core/tools?