Minimum split_fastq value is 250

[adamrtalbot]

Description of the bug

The minimum value for split_fastq is 250 because this the smallest value accepted by FASTP is 1000 but this isn't reflected in the schema. Discovered while trying to fix #1357.

This could be addressed in the schema.

Command used and terminal output

nextflow run . -profile test_cache,docker --outdir results --split_fastq 249 --test_data_base ~/test-datasets


ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:FASTP (test-test_L2)'

Caused by:
  Process `NFCORE_SAREK:SAREK:FASTP (test-test_L2)` terminated with an error exit status (255)

Command executed:

  [ ! -f  test-test_L2_1.fastq.gz ] && ln -sf test_1.fastq.gz test-test_L2_1.fastq.gz
  [ ! -f  test-test_L2_2.fastq.gz ] && ln -sf test_2.fastq.gz test-test_L2_2.fastq.gz
  fastp \
      --in1 test-test_L2_1.fastq.gz \
      --in2 test-test_L2_2.fastq.gz \
      --out1 test-test_L2_1.fastp.fastq.gz \
      --out2 test-test_L2_2.fastp.fastq.gz \
      --json test-test_L2.fastp.json \
      --html test-test_L2.fastp.html \
       \
       \
       \
      --thread 2 \
      --detect_adapter_for_pe \
      --disable_adapter_trimming      --split_by_lines 996 \
      2> >(tee test-test_L2.fastp.log >&2)
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_SAREK:SAREK:FASTP":
      fastp: $(fastp --version 2>&1 | sed -e "s/fastp //g")
  END_VERSIONS

Command exit status:
  255

Command output:
  (empty)

Command error:
  ERROR: you have enabled splitting output by file lines, the file lines (--split_by_lines) should be >= 1000.

### Relevant files

_No response_

### System information

_No response_

[maxulysse]

actually minimal is 0, but good spot

[adamrtalbot]

Source for fastp v0.23.4: https://github.com/OpenGene/fastp?tab=readme-ov-file#output-splitting

Use -S or --split_by_lines to limit the lines of each file. The last files may have smaller sizes since usually the input file cannot be perfectly divided. The actual file lines may be a little greater than the value specified by --split_by_lines since fastp reads and writes data by blocks (a block = 1000 reads).

[FriederikeHanssen]

Minimal is 0 in the schema, because that turns of any splitting. Is there a way, it can be 0 or >=250 with the schema?

[FriederikeHanssen]

Fixed