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SEQTK_TRIM fails when input files use .fq.gz extension #53
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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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