File "salmon.merged.gene_counts.tsv" Contains Floating-Point Values Instead of Raw Integer Counts

[Aeget1000]

Description of the bug

Dear nf-core team,

First of all, I would like to express my gratitude for this incredible community and the nf-core initiative as a cornerstone for reproducibility in computational biology.

I am reaching out to highlight an issue I encountered in versions 3.12.0 and 3.18.0.

Specifically, the file "salmon.merged.gene_counts.tsv" does not appear to contain raw integer counts. Instead, it contains what seem to be floating-point values, as illustrated in the screenshot below:

I have attached the relevant files below (v 3.18.0) and am working with the following sample:
SRX1874029 - NCBI SRA

Thank you for your attention to this matter. I look forward to your insights and any potential solutions.

Best regards,
Christian Andersen

Command used and terminal output

Input/output options
  input          : /work/samplesheet_1_sample_peters.csv
  outdir         : results_peters_1_sample_test

Reference genome options
  genome         : GRCh38
  fasta          : s3://ngi-igenomes/igenomes//Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa
  gtf            : s3://ngi-igenomes/igenomes//Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf
  gene_bed       : s3://ngi-igenomes/igenomes//Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.bed
  star_index     : s3://ngi-igenomes/igenomes//Homo_sapiens/NCBI/GRCh38/Sequence/STARIndex/

Alignment options
  pseudo_aligner : salmon

Process skipping options
  skip_gtf_filter: true
  skip_alignment : true
  skip_deseq2_qc : true

Core Nextflow options
  revision       : 3.18.0
  runName        : clever_meninsky
  launchDir      : /work
  workDir        : /tmp/work
  projectDir     : /home/ucloud/.nextflow/assets/nf-core/rnaseq
  userName       : ucloud
  profile        : mamba
  configFiles    :

Relevant files

JobParameters.json
stdout.txt
samplesheet_1_sample_peters.csv

System information

Hardware: Ucloud
OS: Linux