diff --git a/simulate_PBMC.sh b/Run_test.sh similarity index 86% rename from simulate_PBMC.sh rename to Run_test.sh index 7c237ca..3064f01 100644 --- a/simulate_PBMC.sh +++ b/Run_test.sh @@ -22,6 +22,11 @@ if [ ! -d "dataset" ]; then tar -xzf sub_pbmc_datasets.tar.gz fi +# Subset 10 cells from sub_pbmc_matrice for test +if [ ! -f "dataset/test_sub_pbmc_matrice.csv" ]; then + cut -d ',' -f-11 dataset/sub_pbmc_matrice.csv > dataset/test_sub_pbmc_matrice.csv +fi + # Download reference transcriptome if [ ! -f "dataset/Homo_sapiens.GRCh38.cdna.all.fa" ]; then wget -O - https://ftp.ensembl.org/pub/release-112/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz | gzip -d > dataset/Homo_sapiens.GRCh38.cdna.all.fa @@ -47,4 +52,4 @@ echo "* Execute basic workflow" nextflow run main.nf --matrix dataset/sub_pbmc_matrice.csv \ --transcriptome dataset/Homo_sapiens.GRCh38.cdna.all.fa \ --features gene_name \ - --gtf dataset/GRCh38-2020-A-genes.gtf \ No newline at end of file + --gtf dataset/GRCh38-2020-A-genes.gtf