use the gtf and fasta parameters to input references into the pipeline

[GimenaA]

Hello, I'm trying to run the pipeline, but it's not running for me. I only used ./dependencies_linux64.sh because I didn't need to download the reference files since I already have my Drosophila references. Am I using the genome and gtf parameters correctly in my code bellow?

bpipe -p gene=Arc1 -p gtf_ref=/path/to/reference/GTF_files/fromEnsembl/Drosophila_melanogaster.BDGP6.32.106.gtf -p genome=/path/to/reference/BDGP6.32_ensemble/Drosophila_melanogaster.BDGP6.32.dna.toplevel.fa -p results=/path/to/outputdir/ -p threads=4 -p samples=/path/to/bam_files/treatment_sample_rep1_Aligned.sortedByCoord.out.bam /path/to/bam_files/treatment_sample_rep2_Aligned.sortedByCoord.out.bam /path/to/bam_files/treatment_sample_rep3_Aligned.sortedByCoord.out.bam /path/to/bam_files/control_sample_rep1_Aligned.sortedByCoord.out.bam /path/to/bam_files/control_sample_rep2_Aligned.sortedByCoord.out.bam /path/to/bam_files/control_sample_rep3_Aligned.sortedByCoord.out.bam -p a_mem=20000000000 -p g_mem=20000000000

Thank you