Pipeline fails when any sample has zero reads.

[dfornika]

We occasionally have samples where (often due to problems with demultiplexing), the .fastq.gz file contain zero reads. This causes the entire pipeline to fail with an error message like:

Error executing process > 'kraken2 (sample)'

Caused by:
  Missing output file(s) `sample_kraken2_output.tsv` expected by process `kraken2 (sample)`

Command executed:

  printf -- "- process_name: kraken2\n" > sample_kraken2_provenance.yml
  printf -- "  tool_name: kraken2\n  tool_version: $(kraken2 --version | grep 'version' | cut -d ' ' -f 3)\n" >> sample_kraken2_provenance.yml
  printf -- "  database_path: $(readlink -f 2021-05-17_standard)\n" >> sample_kraken2_provenance.yml
  kraken2 --db 2021-05-17_standard --threads 8 --output sample_kraken2_output.tsv --report sample_kraken2_report.txt --paired sample_trimmed_R1.fastq.gz sample_trimmed_R2.fastq.gz

Command exit status:
  0

Command output:
  (empty)

Command error:
  Loading database information... done.
  0 sequences (0.00 Mbp) processed in 0.001s (0.0 Kseq/m, 0.00 Mbp/m).
    0 sequences classified (-nan%)
    0 sequences unclassified (-nan%)

Work dir:
  work/6a/51705a8af0c42f25bbd2ce45abc112