nf-core/pathogensurveillance

FIND_ASSEMBLIES returns error code when no results are found

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#133 opened on Jan 14, 2025

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buggood first issue

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Description

This is low priority, since it does not prevent the pipeline for functioning correctly.

If a taxon is supplied for which there is no data, the following output is produced by datasets summary genome taxon --as-json-lines pseudeurotiaceae > Pseudeurotiaceae.json:

Error: The taxonomy name 'pseudeurotiaceae' (taxid: '34379') is valid, but no genome data is currently available for this taxon.

Use datasets summary genome taxon <command> --help for detailed help about a command.

The exitcode returned is 1, which makes nextflow think the process failed and it retries. In this case, it actually worked, there is just no data, so ideally it would return an exit code of 0 and an empty JSON file. A check should be added to modules/local/find_assemblies.nf for the phrase "is valid, but no genome data is currently available for this taxon" and make an empty JSON file and return exit code 0.

Contributor guide

Research direction
Modify find assemblies.nf to check for the error message 'is valid, but no genome data is currently available' and if found, create an empty JSON file and exit with code 0.
Tech stack
shell
Domain
data
Issue type
Bug
DifficultyEstimated implementation difficulty for a new contributor, from 1 for very small changes to 5 for expert-level work.
1
Estimated timeA rough time range for an experienced contributor to investigate, implement, test, and prepare a pull request.
Under 1 hour
Activity statusHow available the issue appears right now: fresh, active, stale, blocked, or waiting on maintainer input.
Fresh
ClarityHow clearly the issue explains the expected change, acceptance criteria, and next step.
Clear
Prerequisites
NextflowShell
Newbie friendlinessA 1-100 score estimating how approachable this issue is for first-time contributors.
85