From ec1620c4348a7e8217ca7acabccd9aebdfbffc85 Mon Sep 17 00:00:00 2001
From: alihamraoui <hamraoui@bio.ens.psl.eu>
Date: Wed, 18 Sep 2024 14:46:33 +0200
Subject: [PATCH] ADD: add script to run with paper dataset

---
 simulate_PBMC.sh | 50 ++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 50 insertions(+)
 create mode 100644 simulate_PBMC.sh

diff --git a/simulate_PBMC.sh b/simulate_PBMC.sh
new file mode 100644
index 0000000..7c237ca
--- /dev/null
+++ b/simulate_PBMC.sh
@@ -0,0 +1,50 @@
+#!/bin/bash
+
+# Check if main.nf exists
+if [ ! -f "main.nf" ]; then
+    echo "ERROR: cannot found main.nf." >&2
+    exit 1
+fi
+
+# Check if wget is installed
+if [ ! -x "$(command -v wget)" ]; then
+    echo "ERROR: wget is not installed/not in the PATH." >&2
+    exit 1
+fi
+
+# Download dataset
+if [ ! -f "sub_pbmc_datasets.tar.gz" ]; then
+    wget https://zenodo.org/records/12731409/files/sub_pbmc_datasets.tar.gz
+fi
+
+# Untar dataset
+if [ ! -d "dataset" ]; then
+    tar -xzf sub_pbmc_datasets.tar.gz
+fi
+
+# Download reference transcriptome
+if [ ! -f "dataset/Homo_sapiens.GRCh38.cdna.all.fa" ]; then
+    wget -O - https://ftp.ensembl.org/pub/release-112/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz | gzip -d > dataset/Homo_sapiens.GRCh38.cdna.all.fa
+fi
+
+# Download GTF
+if [ ! -f "dataset/GRCh38-2020-A-genes.gtf" ]; then
+    wget -O - https://ftp.ensembl.org/pub/release-112/gtf/homo_sapiens/Homo_sapiens.GRCh38.112.gtf.gz | gzip -d > dataset/GRCh38-2020-A-genes.gtf
+fi
+
+# Download reference genome
+if [ ! -f "dataset/GRCh38-2020-A-genome.fa" ]; then
+    wget -O - https://ftp.ensembl.org/pub/release-112/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz | gzip -d > dataset/GRCh38-2020-A-genome.fa
+fi
+
+# Check if nextflow is in the path
+if [ ! -x "$(command -v nextflow)" ]; then
+    echo "ERROR: nextflow is not installed/not in the PATH." >&2
+    exit 1
+fi
+
+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