Error for single reads during FASTQ linting preprocessing

[cchapus]

Description of the bug

Hi,

I've tried the new release 3.18.0 with my single read RNA-seq. Happy to test the fact that I can use pre-prepared sortmerna files.

But it failed each time at the step process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT.

I looked at the .command.sh corresponding file:

fq lint \ --disable-validator P001 \ XXXXX.fastq.gz > XXXXX.fq_lint.txt.

But fq lint is for validating a FASTQ file pair. I've single read files.

I've solved it by adding skip_linting: true to the params_file

Command used and terminal output

command:
nextflow run \
/path/Nextflow/nf-core-rnaseq/3_18_0/ \
-profile singularity \
-params-file params_rnaseq_final.yaml

output:
-[nf-core/rnaseq] Pipeline completed with errors-
WARN: Killing running tasks (6)
ERROR ~ Error executing process > 'NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (XXXXX)'

Caused by:
  Process `NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (006_J0)` terminated with an error exit status (1)


Command executed:

  fq lint \
      --disable-validator P001 \
      XXXXX.fastq.gz > XXXXX.fq_lint.txt
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT":
      fq: $(echo $(fq lint --version | sed 's/fq-lint //g'))
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  XXXXX.fastq.gz:2037434:1: [S004] CompleteValidator: empty sequence

Work dir:
  /path/work/9c/d3a299bb8f82445c63c652011ceaed

Container:
  /path/Nextflow/cache/depot.galaxyproject.org-singularity-fq-0.12.0--h9ee0642_0.img

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

 -- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

 -- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

 -- Check '.nextflow.log' file for details

Relevant files

No response

System information

N E X T F L O W ~ version 24.10.3
Linux Ubuntu workstation
container: singularity
nf-core/rnaseq: 3.18.0