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

@pablolopeznie

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@pablolopeznie

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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