spikein_bowtie2 parameter incorrectly assigned to iGenomes Bowtie index when using local spikein_fasta

[tylerstahl]

Description of the bug

When passing a fasta to spikein_fasta param , the spikein_bowtie2 param will get assigned to the default iGenomes bowtie index, instead of constructing a bowtie index with the input fasta

Command used and terminal output

nextflow run nf-core/cutandrun -r 3.2.2 --input samplesheet.csv --outdir results --fasta Homo_sapiens.GRCh38.dna.primary_assembly.fa --gtf Homo_sapiens.GRCh38.115.gtf --peakcaller seacr,macs2 --macs_gsize 2495461690 --blacklist GRCh38-blacklist.bed --use_control true --spikein_fasta Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa --normalisation_mode Spikein --skip_heatmaps --skip_preseq --save_spikein_aligned --skip_dt_qc -resume


Reference data options
  gtf                 : Homo_sapiens.GRCh38.115.gtf
  blacklist           : GRCh38-blacklist.bed
  spikein_bowtie2     : s3://ngi-igenomes/igenomes//Escherichia_coli_K_12_MG1655/NCBI/2001-10-15/Sequence/Bowtie2Index/
  spikein_fasta       : Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa
  fasta               : Homo_sapiens.GRCh38.dna.primary_assembly.fa

Relevant files

No response

System information

Nextflow version: 24.10.4
Hardware: HPC
Executor: SLURM
Container engine: Singularity
OS: Linux
Version of nf-core/cutandrun: 3.2.2