Indexing only run does not produce all indexes when using skip_alignment option

[pmoris]

Description of the bug

The docs recommend running --skip_alignment in conjunction with --save_reference, to do an indexing only run.

From my (minimal) testing, this does not actually run/save the desired (STAR) index process, only a salmon and rsem one.

It does create a salmon index (as part of the infer strandedness thingie?) and an rsem one (even though I'm using the option --aligner star_salmon ...it happens somewhere in the PREPARE_GENOME processes I believe, and ends up containing a duplicate of the .fa file in the main genome output dir).

Command used and terminal output

Command:

nextflow run nf-core/rnaseq \
    -r 3.18.0 \
    --input "./samplesheet.csv" \
    --outdir "./results" \
    --fasta "./GCA_949152365.1_PVPAM_genomic.fna.gz" \
    --gtf "./GCA_949152365.1_PVPAM_genomic.gtf.gz" \
    --aligner star_salmon \
    --save_reference \
    --skip_alignment \
    -profile vsc_calcua,single_node


Output:

results/
├── fastqc
│   ├── raw
│   └── trim
├── fq_lint
│   └── raw
├── genome
│   ├── GCA_949152365.1_PVPAM_genomic.filtered.bed
│   ├── GCA_949152365.1_PVPAM_genomic.filtered.gtf
│   ├── GCA_949152365.1_PVPAM_genomic.fna
│   ├── GCA_949152365.1_PVPAM_genomic.fna.fai
│   ├── GCA_949152365.1_PVPAM_genomic.fna.sizes
│   ├── GCA_949152365.1_PVPAM_genomic.gtf
│   ├── genome.transcripts.fa
│   ├── index
│   └── rsem
├── multiqc
│   ├── multiqc_report_data
│   ├── multiqc_report.html
│   └── multiqc_report_plots
├── pipeline_info
...
└── trimgalore
    ├── reads_trimmed_1.fastq.gz_trimming_report.txt
    └── reads_trimmed_2.fastq.gz_trimming_report.txt

Relevant files

samplesheet.csv

sample,fastq_1,fastq_2,strandedness
reads,/scratch/antwerpen/203/vsc20380/test-area/nf-core-rnaseq-index-only/fastq/reads_R1.fastq.gz,/scratch/antwerpen/203/vsc20380/test-area/nf-core-rnaseq-index-only/fastq/reads_R2.fastq.gz,forward

download PvPAM reference genome and annotation

wget "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/949/152/365/GCA_949152365.1_PVPAM/GCA_949152365.1_PVPAM_genomic.fna.gz"
wget "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/949/152/365/GCA_949152365.1_PVPAM/GCA_949152365.1_PVPAM_genomic.gtf.gz"

System information

nextflow version 24.10.2.5932
slurm + apptainer
Rocky Linux release 8.10 (Green Obsidian)
HPC