nf-core/sarek

No status is 0 - but contains tumor only sample error message

Open

#1,685 opened on Oct 11, 2024

View on GitHubContributor guide
 (5 comments) (0 reactions) (0 assignees)Nextflow (539 forks)auto 404
bughelp wanted

Repository metrics

Stars
 (589 stars)
PR merge metrics
 (PR metrics pending)

Description

Description of the bug

The sample-sheet only contains tumor-samples, but the following tools, which were requested by the option "tools", expect at least one normal-sample : deepvariant, haplotypecaller

while running with a samplesheet with no status and these tools

Command used and terminal output

No response

Relevant files

No response

System information

No response

Contributor guide

Research direction
Locate the sample sheet validation code and trace how the normal sample requirement is enforced for the tools listed. Consider modifying the validation to allow only tumor samples when appropriate tools are not selected.
Tech stack
None
Domain
data
Issue type
Bug
DifficultyEstimated implementation difficulty for a new contributor, from 1 for very small changes to 5 for expert-level work.
2
Estimated timeA rough time range for an experienced contributor to investigate, implement, test, and prepare a pull request.
1-3 hours
Activity statusHow available the issue appears right now: fresh, active, stale, blocked, or waiting on maintainer input.
Active
ClarityHow clearly the issue explains the expected change, acceptance criteria, and next step.
Clear
Prerequisites
Git
Newbie friendlinessA 1-100 score estimating how approachable this issue is for first-time contributors.
75