Submission for Practical Work

D.Puthier/Snakefile

-# Librairie
+# Library
 import os
 import re
 import sys
 
-#Definir le répértoir de travail
+# Define the working directory
 workdir:os.getcwd()
 
-# Définition des chemins de fichiers et répertoires
+# Define file paths and directories
 DATADIR="/shared/projects/2427_data_master/datasets/E-MTAB-8560/"
 STARINDEX="/shared/bank/mus_musculus/mm10/star-2.7.5a"
 
 GTF ="/shared/bank/mus_musculus/mm10/gff/Mus_musculus.GRCm38.97.gtf"
 SZ="/shared/bank/mus_musculus/mm10/star-2.7.5a/chrNameLength.txt"
 
-# Extraction et traitement des noms d'échantillons
+# Extract and process sample names
 SAMPLE=os.listdir(DATADIR)
 SAMPLE=[x for x in SAMPLE if ".fq.gz" in x]
 SAMPLE=[re.sub("_R[12]\\.fq\\.gz","",x)for x in SAMPLE]
@@ -22,7 +22,7 @@ SAMPLE=sorted(SAMPLE)
 
 SAMPLE=SAMPLE[:10]
 
-# Règle principale pour définir les sorties globales
+# Main rule to define global outputs
 rule final:
 	input:  expand("fastqc/{smp}_R1_fastqc.zip" , smp=SAMPLE), \
 			expand("fastqctrim/{smp}_R1_fastqc.zip" , smp=SAMPLE) , \
@@ -127,4 +127,4 @@ rule feature:
 	module load subread/2.0.6 
 	featureCounts -p --countReadPairs -t exon -g gene_id -a {params.gtf} \
 	-o featurecounts/{wildcards.smp}.txt {input}
-	"""
\ No newline at end of file
+	"""