#! /bin/bash
#SBATCH --cpus-per-task=4
#SBATCH --mem=16g
#SBATCH --time=96:00:00
#SBATCH --mail-type=BEGIN,TIME_LIMIT_90,END
#SBATCH --mail-user=capaldobj@nih.gov

module load nextflow

nextflow run nf-core/rnasplice \
-resume \
--input 'sample-input-rna-splice-2024-october-09.csv' \
--contrasts 'contrasts-2024-october-09.csv' \
--miso_genes RUNX1 \
-profile biowulf \
--gtf /fdb/igenomes_nf/Homo_sapiens/Ensembl/pub/release-110/gtf/Homo_sapiens.GRCh38.110.gtf \
--fasta /fdb/igenomes_nf/Homo_sapiens/Ensembl/pub/release-110/fasta/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa \
--star_index /fdb/igenomes_nf/Homo_sapiens/Ensembl/pub/release-110/STARindex/ \
--igenomes_ignore --genome null \
--max_time 72.h \
--outdir 'grch38-rna-seq-splice-results-2024-october-09'