From f5e9f4e52b9213227633654a44e5d9831c18c8a8 Mon Sep 17 00:00:00 2001
From: Hamraoui Ali <72599648+alihamraoui@users.noreply.github.com>
Date: Mon, 21 Oct 2024 12:38:29 +0200
Subject: [PATCH] Update and rename simulate_PBMC.sh to Run_test.sh

---
 simulate_PBMC.sh => Run_test.sh | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)
 rename simulate_PBMC.sh => Run_test.sh (86%)

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