One of the input files that Salmon requires is a transcriptome file, which is not the full genome assembly. The transcriptome file is created from the genome assembly and the annotation file. The transcriptome file contains only the cDNA transcripts of expressed genes. For the Tair10 Arabidopsis genome assembly, the transcriptome file is available to download. For most other genome assemblies, the transcriptome file is not available and you'll have to make it. Here is the code to make a transcriptome file.
#!/bin/tcsh
#BSUB -J M82_DNT #job name
#BSUB -n 20 #number of threads
#BSUB -W 2:0 #time for job to complete
#BSUB -R "rusage[mem=20000]" #to request a node with 20MB of memory
#BSUB -o M82_DNT.%J.out #output file
#BSUB -e M82_DNT.%J.err #error file
module load conda
conda activate /usr/local/usrapps/bitcpt/gffread
set dir=/share/bitcpt/Fall2022/referenceGenomes/Solanum_lycopersicum/M82_vTS3
set gen=M82vTS3
# M82vTS3.agat.gtf
# M82vTS3_assembly.fasta
#gffread -w output.fa -g genome.fa genome.gtf
gffread -w ${dir}/${gen}_transcriptome.fasta -g ${dir}/${gen}_assembly.fasta ${dir}/${gen}.agat.gtf