Allow a prepared ENA metadata samplesheet as input
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- Dominant language
- Nextflow
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- Forks
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- Avg merge
- 1d 18m
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Description
Description of feature
I've created a branch https://github.com/nf-core/fetchngs/tree/skip-runinfo where one can skip the first step. So instead of providing a list of IDs for which metadata is fetched, provide the metadata directly as input and skip that step. It works but was just a quick hack. If this is a generally desirable feature I can code it up in a better way. Maybe using input_type == 'metadata' instead of a new skip_runinfo parameter.
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
Start by reviewing the skip-runinfo branch and the current input handling around the proposed input_type and skip_runinfo options. Confirm how a prepared ENA metadata samplesheet should enter the workflow, ensure the metadata-fetching step is skipped, and verify that the existing downstream fetch process still works with this input.
Written by the indexing model from the issue text.
Assessment
- Domain
- data-engineering
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100