Delete ProjetT-Pip-RNAseq_v2

Scripts/ProjetT-Pip-RNAseq_v2

-# Importation des librairies glob, sys, et re
-import glob,sys,re
-
-## appel du fichier de config
-configfile: "configPT.yaml"
-
-## Definition des variables "constantes" à partir du fichier config (attention aux arborescences dans le yaml)
-REFERENCE_DIR = config['REFERENCE']
-FASTA_REF= config['FASTA']
-GFF_REF= config['GFF']
-GTF_REF= config['GTF']
-READS_DIR = config['READS']
-FASTQC_DIR = config['FASTQC']
-FASTQSCREEN_DIR = config['FASTQSCREEN']
-FASTP_DIR = config['FASTP']
-FASTQC_AF_DIR = config['FASTQC_AF']
-MULTIQC_DIR = config['MULTIQC']
-INDEX_DIR = config['INDEX']
-INDEX_STAR_DIR = config['INDEX_STAR']
-MAPPINGH_DIR = config['MAPPINGH']
-MAPPINGS_DIR = config['MAPPING_STAR']
-BAM_DIR = config['BAMFILES']
-STATS_DIR = config['STATS']
-FILTER_DIR = config['FILTER']
-DUPL_DIR = config['DUPL']
-HTSEQ_DIR = config['HTSEQ']
-STRINGTIE_DIR = config['STRINGTIE']
-STRINGTIECC_DIR = config['STRINGTIECC']
-PREPDE = config['PREPDE']
-NREADS= config['NREADS']
-
-#Wild cards
-REFERENCE, = glob_wildcards(f"{REFERENCE_DIR}{{reference}}.fasta")
-ANNOTATION, = glob_wildcards(f"{REFERENCE_DIR}{{annotation}}.gff")
-READS, = glob_wildcards(f"{READS_DIR}{{reads}}_r1.fastq.gz")
-#SAMPLEFQ, = glob_wildcards(f"{FASTQC_DIR}{{samplefq}}.html")
-#SAMPLEFS, = glob_wildcards(f"{FASTQSCREEN_DIR}{{samplefs}}.html")
-#SAMPLEFQAF, = glob_wildcards(f"{FASTQC_AF_DIR}{{samplefqaf}}.html")
-#SAMPLEFP, = glob_wildcards(f"{FASTP_DIR}{{samplefp}}.html")
-#BAM, = glob_wildcards(f"{BAM_DIR}{{bam}}.bam")
-
-
-# Regle finale pour vérifier la présence des outputs et si ils sont présents ils ne lancent pas le job
-rule final:
-     input:
-          out_fastqc = expand(f"{FASTQC_DIR}{{reads}}_r1_fastqc.html", reads = READS),
-          out_fastqs = expand(f"{FASTQSCREEN_DIR}{{reads}}_r1_screen.html", reads = READS),
-          out_fastp = expand(f"{FASTP_DIR}{{reads}}_report_fastp.html", reads = READS),
-          out_fastqc_af = expand(f"{FASTQC_AF_DIR}{{reads}}_r1_paired_fastqc.html", reads = READS),
-          out_multiqc = expand(f"{MULTIQC_DIR}multiqc_report.html"),
-          out_hisat_idx = expand(f"{INDEX_DIR}P.Falci_3D7"),
-          out_hisat_map = expand(f"{MAPPINGH_DIR}{{reads}}_HISAT.bam" , reads = READS),
-          out_star_map = expand(f"{MAPPINGS_DIR}{{reads}}Aligned.sortedByCoord.out.bam" , reads = READS),
-          out_bam_sort = expand(f"{BAM_DIR}{{reads}}_STAR_sort.bam", reads = READS),
-          out_bam_filt = expand(f"{FILTER_DIR}{{reads}}_STAR_sort_mapped.bam", reads = READS),
-          out_bam_index = expand(f"{BAM_DIR}{{reads}}_STAR_sort.bam.bai", reads = READS),
-          out_bam_stats = expand(f"{STATS_DIR}{{reads}}_STAR_sort_flagstat.txt", reads = READS),
-          #out_bam_md = expand(f"{DUPL_DIR}{{reads}}_HISAT_sort_mapped_markdup_metric.txt", reads = READS),
-          out_htseq = expand(f"{HTSEQ_DIR}HISAT/{{reads}}.txt", reads = READS),
-          #out_gtf_list = expand(f'{STRINGTIE_DIR}STRINGTIE_MERGE/STAR_gtf_list.txt'),
-          #out_stringtie = expand(f'{STRINGTIE_DIR}STRINGTIE_MERGE/STAR_stringtie_merged.gtf'),
-          out_stringtiecc = expand(f'{STRINGTIECC_DIR}STAR/{{reads}}/{{reads}}.gtf', reads=READS),
-          out_gtf_list = expand(f'{STRINGTIECC_DIR}HISAT_gtf_list.txt', reads=READS),
-          out_csv = f'{STRINGTIECC_DIR}HISAT_transcript_count_matrix.csv'
-
-# FastQC before filtering
-rule fastqc:
-     """ 
-          FastQC - Control Quality of reads
-     """
-     threads:4
-     params:
-          out_fastqc=directory(f"{FASTQC_DIR}")
-     input:
-          r1 = f"{READS_DIR}{{reads}}_r1.fastq.gz",
-          r2 = f"{READS_DIR}{{reads}}_r2.fastq.gz"
-     output:
-        out_fastqc_r1 = f"{FASTQC_DIR}{{reads}}_r1_fastqc.html",
-        out_fastqc_r2 = f"{FASTQC_DIR}{{reads}}_r2_fastqc.html",
-        out_fastqc_r1_zip = f"{FASTQC_DIR}{{reads}}_r1_fastqc.zip",
-        out_fastqc_r2_zip = f"{FASTQC_DIR}{{reads}}_r2_fastqc.zip"
-     message:
-          """
-               input=
-                    r1 = {input.r1}
-                    r2 = {input.r2}
-               threads={threads}
-          """
-     shell:
-          """
-               fastqc -o {params.out_fastqc} -t 4 {input.r1} {input.r2}
-          """
-
-# FastQScreen agaisnt 3D7 and human
-rule fastqscreen:
-     """ 
-          FastQScreen - Control Quality of reads
-     """
-     threads:4
-     priority:10000000000000000
-     params:
-          out_fastqs=directory(f"{FASTQSCREEN_DIR}")
-     input:
-          r1 = f"{READS_DIR}{{reads}}_r1.fastq.gz",
-          r2 = f"{READS_DIR}{{reads}}_r2.fastq.gz"
-     output:
-        html_r1= f"{FASTQSCREEN_DIR}{{reads}}_r1_screen.html",
-        html_r2=f"{FASTQSCREEN_DIR}{{reads}}_r2_screen.html",
-        txt_r1=f"{FASTQSCREEN_DIR}{{reads}}_r1_screen.txt",
-        txt_r2=f"{FASTQSCREEN_DIR}{{reads}}_r2_screen.txt",
-     message:
-          """
-               Execute {rule}
-               input=
-                    r1 = {input.r1}
-                    r2 = {input.r2}
-               threads={threads}
-          """
-     shell:
-          """
-               fastq_screen --conf /Users/COHEN/Documents/Logiciels/FastQ-Screen-0.14.1/fastq_screen.conf --aligner BOWTIE2 {input.r1} {input.r2} --outdir {params.out_fastqs}
-          """
-
-# Filtering and trimming with FastP
-rule fastp:
-     """ 
-          FastP - Filtering and trimming before mapping
-     """
-     params:
-          out_fastp=directory(f"{FASTP_DIR}")
-     input:
-          r1 = f"{READS_DIR}{{reads}}_r1.fastq.gz",
-          r2 = f"{READS_DIR}{{reads}}_r2.fastq.gz"
-     output:
-          out_paired_r1 = f"{FASTP_DIR}{{reads}}_r1_paired.fastq.gz",
-          out_unpaired_r1 = f"{FASTP_DIR}{{reads}}_r1_unpaired.fastq.gz",
-          out_paired_r2 = f"{FASTP_DIR}{{reads}}_r2_paired.fastq.gz",
-          out_unpaired_r2 = f"{FASTP_DIR}{{reads}}_r2_unpaired.fastq.gz",
-          out_report= f"{FASTP_DIR}{{reads}}_report_fastp.html",
-          out_json= f"{FASTP_DIR}{{reads}}_fastp.json"
-
-     message:
-          """
-               input={input.r1},{input.r2}
-          """
-     shell:
-          """
-               fastp --in1 {input.r1} --in2 {input.r2} --out1 {output.out_paired_r1} --out2 {output.out_paired_r2}  --unpaired1 {output.out_unpaired_r1} --unpaired2 {output.out_unpaired_r2} -w 1 -h {output.out_report} -j {output.out_json}  
-          """
-
-# FastQC after filtering
-rule fastqc_af:
-     """ 
-          FastQC - Control Quality of reads after FastP
-     """
-     priority:100000000000000
-     params:
-          out_fastqc_af = directory(f"{FASTQC_AF_DIR}")
-     input:
-          r1 = f"{FASTP_DIR}{{reads}}_r1_paired.fastq.gz",
-          r2 = f"{FASTP_DIR}{{reads}}_r2_paired.fastq.gz"
-     output:
-          out_fastqc_af_r1 = f"{FASTQC_AF_DIR}{{reads}}_r1_paired_fastqc.html",
-          out_fastqc_af_r2 = f"{FASTQC_AF_DIR}{{reads}}_r2_paired_fastqc.html",
-          out_fastqc_af_r1_zip = f"{FASTQC_AF_DIR}{{reads}}_r1_paired_fastqc.zip",
-          out_fastqc_af_r2_zip = f"{FASTQC_AF_DIR}{{reads}}_r2_paired_fastqc.zip"
-     message:
-          """
-               input={input.r1},{input.r2}
-          """
-     shell:
-          """
-               fastqc -o {params.out_fastqc_af} -t 4 {input.r1} {input.r2}
-          """
-
-# FastQScreen agaisnt 3D7 and human
-rule multi_qc:
-    """
-    MultiQC
-    """
-    params:
-        out_multi = directory(f"{MULTIQC_DIR}")
-    input:
-        expand(f"{FASTQSCREEN_DIR}{{reads}}_r1_screen.html", reads = READS),
-        expand(f"{FASTQSCREEN_DIR}{{reads}}_r2_screen.html", reads = READS),
-        expand(f"{FASTQSCREEN_DIR}{{reads}}_r1_screen.txt", reads = READS),
-        expand(f"{FASTQSCREEN_DIR}{{reads}}_r2_screen.txt", reads = READS),
-        expand(f"{FASTQC_DIR}{{reads}}_r1_fastqc.html", reads=READS),
-        expand(f"{FASTQC_DIR}{{reads}}_r2_fastqc.html", reads=READS),
-        expand(f"{FASTQC_DIR}{{reads}}_r1_fastqc.zip", reads=READS),
-        expand(f"{FASTQC_DIR}{{reads}}_r2_fastqc.zip", reads=READS),
-        expand(f"{FASTQC_AF_DIR}{{reads}}_r1_paired_fastqc.html", reads=READS),
-        expand(f"{FASTQC_AF_DIR}{{reads}}_r2_paired_fastqc.html", reads=READS),
-        expand(f"{FASTQC_AF_DIR}{{reads}}_r1_paired_fastqc.zip", reads=READS),
-        expand(f"{FASTQC_AF_DIR}{{reads}}_r2_paired_fastqc.zip", reads=READS),
-        expand(f"{FASTP_DIR}{{reads}}_report_fastp.html", reads=READS),
-        expand(f"{FASTP_DIR}{{reads}}_fastp.json",reads=READS)
-
-    output:
-        f"{MULTIQC_DIR}multiqc_report.html",
-    shell:
-        """
-             multiqc {input} -o {params.out_multi}
-        """
-
-# Indexing of 3D7 genome (environ 1 min)
-rule hisat2_index:
-    """                                                                                                                                                                                       
-    Make index with HISAT2 for 3D7                                                                                                                                                 
-    """
-    input:
-        fasta = f"{FASTA_REF}"
-    output:
-        index = f"{INDEX_DIR}P.Falci_3D7",
-    message:
-        """                                                                                                                                                                                   
-        Execute {rule}                                                                                                                                                                    
-        input:                                                                                                                                                                            
-            fasta : {input.fasta}                                                                                                                                                       
-        output:                                                                                                                                                                           
-            index: {output.index}                                                                                                                     
-        """
-    log:
-        output = f"{INDEX_DIR}LOG/3D7_HISAT-INDEX.o",
-        error = f"{INDEX_DIR}LOG/3D7_HISAT-INDEX.e",
-    shell:
-        """
-        ln -s {input.fasta} {output.index} 1>{log.output} 2>{log.error}
-        /Users/COHEN/Documents/Logiciels/hisat2-2.2.0/hisat2-build {input.fasta} {output.index} --quiet
-        """
-
-# Mapping with HISAT2 on Pf 3D7 (max 2 min par échantillon, total 10 min)
-rule hisat2_map:
-    """
-    Map reads on the genome with HISAT2 on paired end
-    """
-    threads: 4
-    input:
-        reference = rules.hisat2_index.output.index,
-        r1 = f"{FASTP_DIR}{{reads}}_r1_paired.fastq.gz",
-        r2 = f"{FASTP_DIR}{{reads}}_r2_paired.fastq.gz"
-    output:
-        summary = f"{MAPPINGH_DIR}{{reads}}_HISAT_summary.txt",
-        bam = f"{MAPPINGH_DIR}{{reads}}_HISAT.bam",
-    message:
-        """                                                                                                                                                                            
-        Execute {rule}                                                                                                                                                                   
-        input:                                                                                                                                                                            
-            reference : {input.reference}
-            R1 : {input.r1}
-            R2 : {input.r2}                                                                                                                                                       
-        output:                                                                                                                                                                           
-            bam: {output.bam}                                                                                                 
-        """
-    shell:
-        """
-        /Users/COHEN/Documents/Logiciels/hisat2-2.2.0/hisat2 -p {threads} -x {input.reference} -1 {input.r1} -2 {input.r2} --summary-file {output.summary} | samtools view -S -b >{output.bam} 
-        """
-
-#Convert GFF in GTF with gffread for RNA-STAR
-rule gff_to_gtf:
-    """                                                                                                                                                                                       
-    Convert GFF in GTF for RNA-STAR                                                                                                                                                 
-    """
-    threads: 8
-    input:
-        gff = f"{REFERENCE_DIR}{{annotation}}.gff"
-    output:
-        gtf = f"{REFERENCE_DIR}{{annotation}}.gtf"
-    message:
-        """                                                                                                                                                                                   
-        Execute {rule}                                                                                                                                                                    
-        input:                                                                                                                                                                            
-            gff : {input.gff}                                                                                                                                                       
-        output:                                                                                                                                                                           
-            gtf: {output.gtf}                                                                                                                     
-        """
-    shell:
-        """
-        /Users/COHEN/Documents/Logiciels/gffread-0.12.2.OSX_x86_64/gffread {input.gff} -T -o {output.gtf}
-        """
-
-#Indexing for RNA-STAR (environ 2 min)
-rule star_index:
-    """
-    Make index with STAR for 3D7
-    """
-    threads: 4
-    params:
-        dir = directory(f"{INDEX_STAR_DIR}")
-    input:
-        fasta = f"{FASTA_REF}",
-        gtf = f"{GTF_REF}",
-    output:
-        index = f"{INDEX_STAR_DIR}Log.out",
-    message:
-        """
-        Execute {rule}
-        input:
-            fasta : {input.fasta}
-            gtf : {input.gtf}
-        output:
-            index: {output.index}
-        """
-    shell:
-        """
-        ln -s {input.fasta} {output.index}
-        /Users/COHEN/Documents/Logiciels/STAR-2-7-5c/bin/MacOSX_x86_64/STAR --runMode genomeGenerate --runThreadN {threads} --genomeDir {params.dir} --genomeFastaFiles {input.fasta} --sjdbGTFfile {input.gtf}
-   
-        """
-
-#Mapping with RNA-STAR on Pf 3D7 (environ 10 min par échantillon, total 1h)
-rule star_mapping:
-    """
-    Map reads on the genome with STAR on paired end
-    """
-    threads: 4
-    params:
-        idx = directory(f"{INDEX_STAR_DIR}"),
-        bam = f"{MAPPINGS_DIR}{{reads}}"
-    input:
-        idx = rules.star_index.output.index,
-        gtf = f"{GTF_REF}",
-        r1 = f"{FASTP_DIR}{{reads}}_r1_paired.fastq.gz",
-        r2 = f"{FASTP_DIR}{{reads}}_r2_paired.fastq.gz"
-    output:
-        bam = f"{MAPPINGS_DIR}{{reads}}Aligned.sortedByCoord.out.bam"
-    message:
-        """
-        Execute {rule}
-        input:
-            idx : {params.idx}
-            gtf : {input.gtf}
-            reads : 
-                r1: {input.r1}
-                r2: {input.r2}
-        output:
-            bam: {output.bam}
-        """
-    shell:
-        """
-        /Users/COHEN/Documents/Logiciels/STAR-2-7-5c/bin/MacOSX_x86_64/STAR --runThreadN 4 --genomeDir {params.idx} --readFilesIn {input.r1} {input.r2} --readFilesCommand gunzip -c --outFileNamePrefix {params.bam} --outSAMtype BAM SortedByCoordinate --sjdbGTFfile {input.gtf} 
-        """
-
-#Sort the BAM files with samtools
-rule bam_sort:
-    """
-    Sort the BAM files     
-    """
-    threads: 4
-    input:
-        star =f'{MAPPINGS_DIR}{{reads}}Aligned.sortedByCoord.out.bam',
-        hisat = f"{MAPPINGH_DIR}{{reads}}_HISAT.bam"
-    output:
-        out_star = f"{BAM_DIR}{{reads}}_STAR_sort.bam",
-        out_hisat = f"{BAM_DIR}{{reads}}_HISAT_sort.bam"
-    message:
-        """
-        Execute {rule}
-        input:
-            star : {input.star}
-            hisat : {input.hisat}
-        output:
-            bam: {output.out_star}, {output.out_hisat}
-        """
-    shell:
-        """
-        samtools sort  {input.star} > {output.out_star};
-        samtools sort  {input.hisat} > {output.out_hisat}
-        """
-
-#Filtering of the BAM files with samtools
-rule bam_filter:
-    """
-    Filtering BAM files      
-    """
-    threads: 4
-    input:
-        star_bam = f"{BAM_DIR}{{reads}}_STAR_sort.bam",
-        hisat_bam = f"{BAM_DIR}{{reads}}_HISAT_sort.bam"
-    output:
-        mapped_star = f"{FILTER_DIR}{{reads}}_STAR_sort_mapped.bam",
-        unmapped_star = f"{FILTER_DIR}{{reads}}_STAR_sort_unmapped.bam",
-        mapped_hisat = f"{FILTER_DIR}{{reads}}_HISAT_sort_mapped.bam",
-        unmapped_hisat = f"{FILTER_DIR}{{reads}}_HISAT_sort_unmapped.bam"
-    message:
-        """
-        Execute {rule}
-        input: {input.star_bam}
-        
-        """
-    shell:
-        """
-        samtools view -b -F 4 {input.star_bam} > {output.mapped_star}
-        samtools view -b -f 4 {input.star_bam} > {output.unmapped_star}
-        samtools view -b -F 4 {input.hisat_bam} > {output.mapped_hisat}
-        samtools view -b -f 4 {input.hisat_bam} > {output.unmapped_hisat}
-        """
-
-# Identify the duplicates in BAM with Picard tools
-rule bam_markdup:
-    """
-    Mark duplicates in BAM files      
-    """
-    threads: 4
-    #params:
-        # récupérer l'option dans le yaml . voir pour mettre un if . A regarder !!!
-    input:
-         bam_star=f"{FILTER_DIR}{{reads}}_STAR_sort_mapped.bam",
-         bam_hisat = f"{FILTER_DIR}{{reads}}_HISAT_sort_mapped.bam",
-    output:
-        star = f"{DUPL_DIR}{{reads}}_STAR_sort_mapped_markdup.bam",
-        star_txt = f"{DUPL_DIR}{{reads}}_STAR_sort_mapped_markdup_metric.txt",
-        hisat = f"{DUPL_DIR}{{reads}}_HISAT_sort_mapped_markdup.bam",
-        hisat_txt = f"{DUPL_DIR}{{reads}}_HISAT_sort_mapped_markdup_metric.txt"
-    message:
-        """
-        Execute {rule}
-        input: {input.bam_star}, {input.bam_hisat}
-        """
-    shell:
-        """
-        java -jar /Users/COHEN/Documents/Logiciels/picard.jar MarkDuplicates I={input.bam_star} O={output.star} M={output.star_txt}
-        java -jar /Users/COHEN/Documents/Logiciels/picard.jar MarkDuplicates I={input.bam_hisat} O={output.hisat} M={output.hisat_txt}
-        """
-
-#Index the BAM files with samtools
-rule bam_index:
-    """
-    Index BAM files      
-    """
-    threads: 4
-    input:
-        bam_star = f"{BAM_DIR}{{reads}}_STAR_sort.bam",
-        bam_hisat = f"{BAM_DIR}{{reads}}_HISAT_sort.bam",
-        bam_star_filt = f"{FILTER_DIR}{{reads}}_STAR_sort_mapped.bam",
-        bam_hisat_filt =f"{FILTER_DIR}{{reads}}_HISAT_sort_mapped.bam",
-        bam_star_filt_md = f"{DUPL_DIR}{{reads}}_STAR_sort_mapped_markdup.bam",
-        bam_hisat_filt_md = f"{DUPL_DIR}{{reads}}_HISAT_sort_mapped_markdup.bam",
-    output:
-        bai = f"{BAM_DIR}{{reads}}_STAR_sort.bam.bai"
-    message:
-        """
-        Execute {rule}
-        input: {input.bam_star}
-        """
-    shell:
-        """
-        samtools index {input.bam_star}
-        samtools index {input.bam_hisat}
-        samtools index {input.bam_star_filt}
-        samtools index {input.bam_hisat_filt}
-        samtools index {input.bam_star_filt_md}
-        samtools index {input.bam_hisat_filt_md}
-        """
-
-#Stats on the BAM files with samtools
-rule bam_stats:
-    """
-    Statistics data on the BAM files      
-    """
-    threads: 4
-    input:
-        bam_star = f"{BAM_DIR}{{reads}}_STAR_sort.bam",
-        bam_hisat = f"{BAM_DIR}{{reads}}_HISAT_sort.bam",
-        bam_star_filt = f"{FILTER_DIR}{{reads}}_STAR_sort_mapped.bam",
-        bam_hisat_filt =f"{FILTER_DIR}{{reads}}_HISAT_sort_mapped.bam",
-        bam_star_filt_md = f"{DUPL_DIR}{{reads}}_STAR_sort_mapped_markdup.bam",
-        bam_hisat_filt_md = f"{DUPL_DIR}{{reads}}_HISAT_sort_mapped_markdup.bam",
-    output:
-        flagstat_star = f"{STATS_DIR}{{reads}}_STAR_sort_flagstat.txt",
-        flagstat_hisat = f"{STATS_DIR}{{reads}}_HISAT_sort_flagstat.txt",
-        flagstat_star_filt= f"{STATS_DIR}{{reads}}_STAR_sort_mapped_flagstat.txt",
-        flagstat_hisat_filt = f"{STATS_DIR}{{reads}}_HISAT_sort_mapped_flagstat.txt",
-        flagstat_star_filt_md= f"{STATS_DIR}{{reads}}_STAR_sort_mapped_markdup_flagstat.txt",
-        flagstat_hisat_filt_md= f"{STATS_DIR}{{reads}}_HISAT_sort_mapped_markdup_flagstat.txt",
-    message:
-        """
-        Execute {rule}
-        input: {input}
-        """
-    shell:
-        """
-        samtools flagstat {input.bam_star} > {output.flagstat_star}
-        samtools flagstat {input.bam_hisat} > {output.flagstat_hisat}
-        samtools flagstat {input.bam_star_filt} > {output.flagstat_star_filt}
-        samtools flagstat {input.bam_star_filt_md} > {output.flagstat_star_filt_md}
-        samtools flagstat {input.bam_hisat_filt} > {output.flagstat_hisat_filt}
-        samtools flagstat {input.bam_hisat_filt_md} > {output.flagstat_hisat_filt_md}
-        """
-
-#Create the count table from the BAM files with Picard tools
-rule htseq_counts :
-    """
-    Create the count table with HTseq-count      
-    """
-    threads: 4
-    input:
-         bam_star = f"{DUPL_DIR}{{reads}}_STAR_sort_mapped_markdup.bam",
-         bam_hisat = f"{DUPL_DIR}{{reads}}_HISAT_sort_mapped_markdup.bam",
-         gtf = f"{GTF_REF}"
-    output:
-         count_table_star = f"{HTSEQ_DIR}STAR/{{reads}}.txt",
-         count_table_hisat = f"{HTSEQ_DIR}HISAT/{{reads}}.txt"
-    message:
-        """
-        Execute {rule}
-        input: 
-            bam: {input.bam_star}
-            gtf: {input.gtf}
-        output: {output.count_table_star}
-        """
-    shell:
-        """
-        htseq-count -t exon -i gene_id -f bam {input.bam_star} {input.gtf} > {output.count_table_star}
-        htseq-count -t exon -i gene_id -f bam {input.bam_hisat} {input.gtf} > {output.count_table_hisat}
-        """
-
-#Create the count table from the BAM files with Picard tools
-rule stringtie_cc :
-    """
-    Create the count table with HTseq-count
-    """
-    threads: 4
-    input:
-         bam_star = f"{DUPL_DIR}{{reads}}_STAR_sort_mapped_markdup.bam",
-         bam_hisat = f"{DUPL_DIR}{{reads}}_HISAT_sort_mapped_markdup.bam",
-         gtf = f"{GTF_REF}"
-    output:
-         star_gtf = f'{STRINGTIECC_DIR}STAR/{{reads}}/{{reads}}.gtf',
-         hisat_gtf= f'{STRINGTIECC_DIR}HISAT/{{reads}}/{{reads}}.gtf',
-         star_tsv = f'{STRINGTIECC_DIR}STAR/{{reads}}/{{reads}}.tsv',
-         hisat_tsv = f'{STRINGTIECC_DIR}HISAT/{{reads}}/{{reads}}.tsv'
-    message:
-        """
-        Execute {rule}
-        input:
-            bam: {input.bam_star}
-            gtf: {input.gtf}
-        output: {output.star_tsv}
-        """
-    shell:
-        """
-        /Users/COHEN/Documents/Logiciels/stringtie-2.1.4.OSX_x86_64/stringtie -p 8 -G {input.gtf} -e -B -o {output.star_gtf} -A {output.star_tsv} {input.bam_star}
-        /Users/COHEN/Documents/Logiciels/stringtie-2.1.4.OSX_x86_64/stringtie -p 8 -G {input.gtf} -e -B -o {output.hisat_gtf} -A {output.hisat_tsv} {input.bam_hisat}
-
-        """
-
-rule gtf_list:
-    threads : 1
-    input:
-        list_gtf_star = expand(f'{STRINGTIECC_DIR}STAR/{{reads}}/{{reads}}.gtf', reads = READS),
-        list_gtf_hisat = expand(f'{STRINGTIECC_DIR}HISAT/{{reads}}/{{reads}}.gtf', reads = READS),
-        names_reads= f'{NREADS}'
-
-    output :
-        gtf_star = f'{STRINGTIECC_DIR}STAR_gtf_list.txt',
-        gtf_hisat = f'{STRINGTIECC_DIR}HISAT_gtf_list.txt',
-        prep_star = f'{STRINGTIECC_DIR}STAR_gtf_list_prep.txt',
-        prep_hisat = f'{STRINGTIECC_DIR}HISAT_gtf_list_prep.txt'
-    shell:
-        """
-        find {input.list_gtf_star} >> {output.gtf_star} 
-        find {input.list_gtf_hisat} >> {output.gtf_hisat}
-        paste {input.names_reads} {output.gtf_star} | sed "s/\t/ /"  >> {output.prep_star}
-        paste {input.names_reads} {output.gtf_hisat} | sed "s/\t/ /" >> {output.prep_hisat}
-        """
-
-rule stringtie_csv:
-    threads : 1
-    input :
-        mergelist_star = rules.gtf_list.output.prep_star,
-        mergelist_hisat = rules.gtf_list.output.prep_hisat,
-        script = f"{PREPDE}"
-    output :
-        gcsv_star = f'{STRINGTIECC_DIR}STAR_gene_count_matrix.csv',
-        tcsv_star = f'{STRINGTIECC_DIR}STAR_transcript_count_matrix.csv',
-        gcsv_hisat = f'{STRINGTIECC_DIR}HISAT_gene_count_matrix.csv',
-        tcsv_hisat = f'{STRINGTIECC_DIR}HISAT_transcript_count_matrix.csv',
-    shell:
-        """
-        python2 {input.script} -i {input.mergelist_star} -t {output.tcsv_star} -g {output.gcsv_star}
-        python2 {input.script} -i {input.mergelist_hisat} -t {output.tcsv_hisat} -g {output.gcsv_hisat}
-
-       """
\ No newline at end of file