Creates and uses `HISAT2_EXTRACTSPLICESITES` when hisat2_extractsplicesites not specified

Description of the bug

For Bacterial genomes we dont want to use splice sites, while creating HISAT index as well as aligning, even though I dont specify hisat2_extractsplicesites in my nextflow command it creates and try to build index with empty splice site file and end up failing.

Command used and terminal output

nextflow run nf-core-references/main.nf \
        --input datasheet.yaml \
        --outdir ./references_indices \
        --tools "star,salmon,bowtie2,hisat2,kallisto,rsem,faidx,createsequencedictionary" \
        -with-trace

Relevant files

Oct-31 14:21:30.129 [Task submitter] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=NFCORE_REFERENCES:REFERENCES:PREPARE_GENOME_RNASEQ:HISAT2_BUILD (Escherichia_coli_110957_gca_000485615.ASM48561v1_.dna.toplevel.fa); work-dir=/test_analysis/bulk-references/work/eb/aa9add26141404821546e5456628fc
error [nextflow.exception.ProcessFailedException]: Error submitting process 'NFCORE_REFERENCES:REFERENCES:PREPARE_GENOME_RNASEQ:HISAT2_BUILD (Escherichia_coli_110957_gca_000485615.ASM48561v1_.dna.toplevel.fa)' for execution
Oct-31 14:21:30.224 [Task submitter] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_REFERENCES:REFERENCES:PREPARE_GENOME_RNASEQ:HISAT2_BUILD (Escherichia_coli_110957_gca_000485615.ASM48561v1_.dna.toplevel.fa)'

Caused by:
Failed to submit process to grid scheduler for execution

Command executed:

sbatch .command.run

Command exit status:
1

Command output:
sbatch: error: Memory specification can not be satisfied
sbatch: error: Batch job submission failed: Requested node configuration is not available

Command error:
Settings:
Output files: "hisat2/Escherichia_coli_110957_gca_000485615.ASM48561v1_.dna.toplevel..ht2"
Line rate: 7 (line is 128 bytes)
Lines per side: 1 (side is 128 bytes)
Offset rate: 4 (one in 16)
FTable chars: 10
Strings: unpacked
Local offset rate: 3 (one in 8)
Local fTable chars: 6
Local sequence length: 57344
Local sequence overlap between two consecutive indexes: 1024
Endianness: little
Actual local endianness: little
Sanity checking: disabled
Assertions: disabled
Random seed: 0
Sizeofs: void:8, int:4, long:8, size_t:8
Input files DNA, FASTA:
Escherichia_coli_110957_gca_000485615.ASM48561v1_.dna.toplevel.fa
Reading reference sizes
Time reading reference sizes: 00:00:00
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
Time to join reference sequences: 00:00:00
Time to read SNPs and splice sites: 00:00:00
Warning: no variants or splice sites in this graph
Total time for call to driver() for forward index: 00:00:01
Error: Encountered exception: 'Nongraph exception'
Command: hisat2-build --wrapper basic-0 -p 24 --ss Escherichia_coli_110957_gca_000485615.ASM48561v1.62.splice_sites.txt --exon Escherichia_coli_110957_gca_000485615.ASM48561v1.62.exons.txt Escherichia_coli_110957_gca_000485615.ASM48561v1_.dna.toplevel.fa hisat2/Escherichia_coli_110957_gca_000485615.ASM48561v1_.dna.toplevel
Deleting "hisat2/Escherichia_coli_110957_gca_000485615.ASM48561v1_.dna.toplevel.1.ht2" file written during aborted indexing attempt.
Deleting "hisat2/Escherichia_coli_110957_gca_000485615.ASM48561v1_.dna.toplevel.2.ht2" file written during aborted indexing attempt.
Deleting "hisat2/Escherichia_coli_110957_gca_000485615.ASM48561v1_.dna.toplevel.3.ht2" file written during aborted indexing attempt.
Deleting "hisat2/Escherichia_coli_110957_gca_000485615.ASM48561v1_.dna.toplevel.4.ht2" file written during aborted indexing attempt.
Deleting "hisat2/Escherichia_coli_110957_gca_000485615.ASM48561v1_.dna.toplevel.5.ht2" file written during aborted indexing attempt.
Deleting "hisat2/Escherichia_coli_110957_gca_000485615.ASM48561v1_.dna.toplevel.6.ht2" file written during aborted indexing attempt.
Deleting "hisat2/Escherichia_coli_110957_gca_000485615.ASM48561v1_.dna.toplevel.7.ht2" file written during aborted indexing attempt.
Deleting "hisat2/Escherichia_coli_110957_gca_000485615.ASM48561v1_.dna.toplevel.8.ht2" file written during aborted indexing attempt.

Work dir:
/test_analysis/bulk-references/work/eb/aa9add26141404821546e5456628fc

Container:
/nf_singularity/community-cr-prod.seqera.io-docker-registry-v2-blobs-sha256-d2-d2ec9b73c6b92e99334c6500b1b622edaac316315ac1708f0b425df3131d0a83-data.img

System information

Nextflow version (25.10.0)
Hardware ( HPC)
Executor ( slurm)
Container engine: (Singularity)
OS ( Linux, )
Version of nf-core/references (dev)

Start with the NFCORE_REFERENCES:REFERENCES:PREPARE_GENOME_RNASEQ:HISAT2_BUILD process and trace how the hisat2_extractsplicesites parameter reaches the build command. Reproduce the provided bacterial-genome command, then verify that an unspecified parameter does not create or pass empty splice-site or exon inputs and that the HISAT2 index build completes.