rnaseq workflow isn't outputing .merged.gene_counts.tsv

[diegogotex]

Description of the bug

Hi guys,
I'm running the following command using nf-core/rnaseq 3.18.0 on the nextflow 24.20.4:

nextflow run nf-core/rnaseq
--input samplesheet.csv
--outdir ./rnaseq_out
--gtf REF/Canis_lupus_familiaris.ROS_Cfam_1.0.113.gtf
--fasta REF/Canis_lupus_familiaris.ROS_Cfam_1.0.dna.toplevel.fa
--save_unaligned
--pseudo_aligner salmon
-profile singularity
-resume

looking at the rnaseq_out/star_salmon directory, there is only individual folders for each sample, log and samtools_stats, and there is also a tx2gene.tsv file.

all the files are being generated normally by the nf-core/rnaseq 3.17.0.

Thanks.

Command used and terminal output

nextflow run nf-core/rnaseq \
        --input samplesheet.csv \
        --outdir ./rnaseq_out \
        --gtf REF/Canis_lupus_familiaris.ROS_Cfam_1.0.113.gtf \
        --fasta REF/Canis_lupus_familiaris.ROS_Cfam_1.0.dna.toplevel.fa \
        --save_unaligned \
        --pseudo_aligner salmon \
        -profile singularity \
        -resume

Relevant files

No response

System information

Nextflow version: 23.20.4
Hardware: HPC
Executor: slurm
Container engine: Singularity
OS: Linux
Version of nf-core/rnaseq: 3.18.0