tp

dputhier/Makefile

+
+#The list of subcommands
+help:
+	@echo "Avaiable subcommands"
+	@echo "\t- run"
+	@echo "\t- clean"
+
+run:
+	@bash -c "module unload snakemake; \
+	module load snakemake/7.25.0 ; \
+	snakemake --cluster 'sbatch -c {params.cpu} --mem {params.mem} --partition=fast --account=2427_data_master' -c 3000 -j  500  --rerun-incomplete --rerun-trigger mtime"
+
+dry:
+	@bash -c "module unload snakemake; \
+	module load snakemake/7.25.0 ; \
+	snakemake --cluster 'sbatch -c {params.cpu} --mem {params.mem} --partition=fast --account=2427_data_master' -c 3000 -j  500  --rerun-incomplete --rerun-trigger mtime -n -p"
+
+#Clean unnecessary files 
+clean: 
+	@rm -f slurm*.out
+	
+
+graph:
+	@bash -c "module unload snakemake; \
+	module load snakemake/7.25.0 ; \
+	module load graphviz/2.40.1 ; \
+	snakemake --dag | dot -Tpng > graph.png"
+
+rulegraph:
+	@bash -c "module unload snakemake; \
+	module load snakemake/7.25.0 ; \
+	module load graphviz/2.40.1 ; \
+	snakemake --rulegraph | dot -Tpng > rulegraph.png"
+
+queue:
+	@squeue -u $$USER
+
+

dputhier/Snakefile

+
+import os 
+import re
+import sys
+
+WDIR = os.getcwd()
+#print(WDIR)
+
+workdir: WDIR
+
+#print ("Starting workflow")
+
+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"
+
+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]
+SAMPLE = list(set(SAMPLE))
+SAMPLE = sorted(SAMPLE)
+
+#SAMPLE = SAMPLE[:10]
+
+#toto = expand("trimmomatic/{smp}_R1.fq.gz", smp=SAMPLE)
+#print(toto)
+#sys.exit()
+
+rule final:
+	input:  expand("fastqc/{smp}_R1_fastqc.zip", smp=SAMPLE) , \
+			expand("trimmomatic/{smp}_R1.fq.gz", smp=SAMPLE) , \
+			expand("fastqc_trim/{smp}_R1_fastqc.zip" , smp=SAMPLE) , \
+			expand("star/{smp}.bam", smp=SAMPLE) , \
+			expand("star/{smp}.bam.bai", smp=SAMPLE) , \
+			expand("coverage/{smp}.bw", smp=SAMPLE) , \
+			expand("featurecounts/{smp}.txt" , smp=SAMPLE)
+
+rule fastqc:
+	input:  r1 = DATADIR + "{smp}_R1.fq.gz", \
+			r2 = DATADIR + "{smp}_R2.fq.gz"
+	output: r1="fastqc/{smp}_R1_fastqc.zip", \
+			r2="fastqc/{smp}_R2_fastqc.zip"
+	params: cpu="1", mem="4G"
+	shell: """
+	module load fastqc/0.12.1
+	fastqc --outdir fastqc {input.r1} {input.r2}
+	"""
+
+rule trimmomatic:
+	input:  r1 = DATADIR + "{smp}_R1.fq.gz", \
+			r2 = DATADIR + "{smp}_R2.fq.gz"
+	output: r1="trimmomatic/{smp}_R1.fq.gz", \
+			r2="trimmomatic/{smp}_R2.fq.gz", \
+			r1u="trimmomatic/{smp}_R1u.fq.gz", \
+			r2u="trimmomatic/{smp}_R2u.fq.gz"
+	params: cpu="4", mem="4G"
+	shell: """
+	module load trimmomatic/0.39
+	trimmomatic PE -threads 1 -phred33 \
+        {input.r1} {input.r2} \
+        {output.r1} {output.r1u} \
+        {output.r2} {output.r2u} \
+        SLIDINGWINDOW:4:20 MINLEN:20
+	"""
+
+rule fastqc_trim:
+	input:  r1="trimmomatic/{smp}_R1.fq.gz", \
+			r2="trimmomatic/{smp}_R2.fq.gz"
+	output: r1="fastqc_trim/{smp}_R1_fastqc.zip", \
+			r2="fastqc_trim/{smp}_R2_fastqc.zip"
+	params: cpu="1", mem="4G"
+	shell: """
+	module load fastqc/0.12.1
+	fastqc --outdir fastqc_trim {input.r1} {input.r2}
+	"""
+
+rule star:
+	input:  r1="trimmomatic/{smp}_R1.fq.gz", \
+			r2="trimmomatic/{smp}_R2.fq.gz"
+	output: r1="star/{smp}.bam"
+	params: cpu="20", mem="50G", index=STARINDEX
+	shell: """
+	module unload star
+	module load star/2.7.5a
+	STAR  --genomeDir {params.index} \
+	--runThreadN {params.cpu} \
+	--readFilesIn {input.r1} {input.r2} \
+	--outFileNamePrefix star/{wildcards.smp} \
+	--outSAMtype BAM SortedByCoordinate \
+	--readFilesCommand zcat \
+	--outFilterMultimapNmax 1 
+	mv star/{wildcards.smp}Aligned.sortedByCoord.out.bam  {output}
+	"""
+
+rule samtools_index:
+	input: "star/{smp}.bam"
+	output: "star/{smp}.bam.bai"
+	params: cpu="1", mem="4G"
+	shell: """
+	module unload samtools
+	module load samtools/1.18
+	samtools index {input}
+	"""
+
+rule big_wig:
+	input: bam="star/{smp}.bam", bai="star/{smp}.bam.bai"
+	output: "coverage/{smp}.bw"
+	params: cpu="20", mem="50G", sz=SZ
+	shell: """
+	module unload rseqc
+	module unload ucsc-wigtobigwig
+	module load ucsc-wigtobigwig/377
+	module load rseqc/2.6.4
+	mkdir -p coverage
+	bam2wig.py -s {params.sz} -i {input.bam} -o coverage/{wildcards.smp}
+	"""
+
+rule featurecounts:
+	input: bam="star/{smp}.bam"
+	output: "featurecounts/{smp}.txt"
+	params: cpu="4", mem="16G", gtf=GTF
+	shell: """
+	module unload subread 
+	module load subread/2.0.6 
+	mkdir -p featurecounts
+	featureCounts -p --countReadPairs -t exon -g gene_id -a {params.gtf} -o {output} {input.bam}
+	"""