Pipeline fails quietly when input fastqs are not found
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- Dominant language
- Nextflow
- Stars
- 229
- Forks
- 141
- Avg merge
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Description
Description of the bug
When input fastq files in the sample sheet are not found, the pipeline does not display this error in the console/terminal.
The other initial steps like genome indexing still continue, but the fastq error can only be found in the log file.
It will be helpful if the error is shown in the console so that the user can quickly resolve the issue.
Command used and terminal output
Relevant files
No response
System information
This seems as a better order to list the system information, from lowest to highest level.
Version of nf-core/atacseq: 2.1.2
Nextflow version: v24.10.3
Container engine: Docker 27.4.1
OS: Ubuntu 22.04.5 LTS x86_64
Executor: Local
Hardware: Desktop
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 reproducing the pipeline with a sample sheet that names missing FASTQ files and inspect where input validation reports errors. Done means the missing-file error appears in the console before later steps such as genome indexing continue, rather than only in the log file.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100