SEQTK_TRIM fails when input files use .fq.gz extension
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Description
Description of feature
Hi,
I noticed that nf-core/demo (v1.1.0) runs successfully when input files
use the .fastq.gz extension, but fails when using .fq.gz.
The process SEQTK_TRIM completes successfully (exit status 0), but
Nextflow raises:
Missing output file(s) *.fastq.gz
Inspecting the work directory shows that the generated files retain the
.fq.gz extension when the input files use this naming convention.
However, the process output declaration expects *.fastq.gz.
It could be a good idea to support both extensions (e.g. *.{fq,fastq}.gz)
to improve the pipeline robustness.
Environment:
- Pipeline version: 1.1.0
- Nextflow version: 25.10.3
- Profile: docker
Thanks!
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Research direction
Find the SEQTK_TRIM process and inspect its output declaration, then reproduce the issue with inputs ending in .fq.gz. The work is done when the process accepts and reports outputs for both .fq.gz and .fastq.gz naming conventions without a missing-output error.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 2/5
- Estimated time
- 1-3 hours
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 50/100