tp

D.Puthier/Makefile

+#The list of subcommands
+
+help:
+	@echo "Available subcommands"
+	@echo "\t- run"
+	@echo "\t- dry"
+	@echo "\t- clean"
+	@echo "\t- graph"
+	@echo "\t- rulegraph"
+	@echo "\t- queue"
+
+# To start the workflow
+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

D.Puthier/Snakefile

+#singularity: "docker://continuumio/miniconda3:4.4.10"
+import os
+import re
+import sys
+
+workdir:os.getcwd()
+
+DIR="/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(DIR)
+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]
+
+rule all:
+	input:  expand("fastqc/{smp}_R1_fastqc.zip" , smp=SAMPLE), \
+			expand("fastqctrim/{smp}_R1_fastqc.zip" , smp=SAMPLE) , \
+			expand("star/{smp}.bam.bai" , smp=SAMPLE) , \
+			expand("coverage/{smp}.bw" , smp=SAMPLE) , \
+			expand("featurecounts/{smp}.txt" , smp=SAMPLE) , \
+			expand("star/{smp}.bam" , smp=SAMPLE)
+
+rule fastqc:
+	input:  r1 = DIR + "{smp}_R1.fq.gz", \
+			r2 = DIR + "{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 = DIR + "{smp}_R1.fq.gz", \
+			r2 = DIR + "{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 ="fastqctrim/{smp}_R1_fastqc.zip", \
+			r2 ="fastqctrim/{smp}_R2_fastqc.zip"
+	params : cpu="1" , mem="4G"
+	shell:"""
+	module load fastqc/0.12.1
+	fastqc  --outdir fastqctrim {input.r1} {input.r2}
+	"""
+
+rule star:
+	input:  r1="trimmomatic/{smp}_R1.fq.gz", \
+			r2="trimmomatic/{smp}_R2.fq.gz"
+	output: "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: "star/{smp}.bam"
+	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} \
+	-o coverage/{wildcards.smp}
+	"""
+
+rule feature_counts:
+	input: "star/{smp}.bam"
+	output: "featurecounts/{smp}.txt"
+	params: cpu="4" , mem="16G" , gtf=GTF
+	shell:"""
+	module unload subread 
+	module load subread/2.0.6 
+	featureCounts -p --countReadPairs -t exon -g gene_id -a {params.gtf} \
+	-o featurecounts/{wildcards.smp}.txt {input}
+	"""
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