diff --git a/D.Puthier/Snakefile b/D.Puthier/Snakefile index 872e43156a16cf8664978b757f81b9c5f4b76f40..34298bdde9b8c192858d1a66bcdfecef7abcf7a3 100644 --- a/D.Puthier/Snakefile +++ b/D.Puthier/Snakefile @@ -1,19 +1,19 @@ -# 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 + """