Empty files were also published from the module samtools/fastq

[LilyAnderssonLee]

Description of the bug

A bug was found in Taxprofiler versions newer than 1.0.1. Three FASTQ files were published by the module samtools/fastq after converting the unmapped human reads BAM file generated from minimap2, and two of them are empty. All these three files were passed to the classifiers and it causes errors.

Files under the folder results/samtools/fastq

-rw-rw----+ 1 lili.li users 28 Jan 19 10:34 sample1.unmapped_1.fastq.gz
-rw-rw----+ 1 lili.li users 55M Jan 19 10:34 sample1.unmapped_other.fastq.gz
-rw-rw----+ 1 lili.li users 28 Jan 19 10:34 sample.unmapped_singleton.fastq.gz

Error message:

Command executed:

  kraken2 \
      --db k2_pluspf_20230605 \
      --threads 12 \
      --report sample1_k2_pluspf.kraken2.kraken2.report.txt \
      --gzip-compressed \
      --unclassified-out sample1_k2_pluspf.kraken2.unclassified.fastq \
      --classified-out sample1_k2_pluspf.kraken2.classified.fastq \
      --output /dev/null \
       \
       \
      sample1.unmapped_1.fastq.gz
  
  pigz -p 12 *.fastq
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_TAXPROFILER:TAXPROFILER:PROFILING:KRAKEN2_KRAKEN2":
      kraken2: $(echo $(kraken2 --version 2>&1) | sed 's/^.*Kraken version //; s/ .*$//')
      pigz: $( pigz --version 2>&1 | sed 's/pigz //g' )
  END_VERSIONS

Command exit status:
  0

Command output:
  (empty)

Command error:
  Loading database information... done.
  0 sequences (0.00 Mbp) processed in 0.040s (0.0 Kseq/m, 0.00 Mbp/m).
    0 sequences classified (-nan%)
    0 sequences unclassified (-nan%)
  pigz: skipping: *.fastq does not exist

Command used and terminal output

nextflow run nf-core/taxprofiler -r 1.1.2 -profile hasta,singularity --input cases/20231227/samplesheet_20231227.csv --databases cases/20231227/databases_20231227.csv --outdir results/20231227 --save_preprocessed_reads --perform_longread_qc --longread_qc_skipqualityfilter --perform_longread_hostremoval --hostremoval_reference references/GCF_000001405.39_GRCh38.p13_genomic.fna --save_hostremoval_index --save_hostremoval_unmapped --run_kraken2 --kraken2_save_reads --kraken2_save_readclassification --run_centrifuge --centrifuge_save_reads --run_krona -params-file scripts/params.json -resume

Relevant files

No response

System information

Taxprofiler V.1.1.2