diff --git a/Snakefile b/Snakefile
index ff6071b47a4d1be8e1fe70750296b5edb5325908..2f9142b94fecc872d1f58aa255181fb54289509d 100755
--- a/Snakefile
+++ b/Snakefile
@@ -69,7 +69,10 @@ else:
 
 
 sample_dir = config["input_dir"]
+
 analysis_dir = config["analysis_dir"]
+if not os.path.exists(analysis_dir):
+    os.makedirs(analysis_dir)
 
 input_data = [sample_dir + "/{{SAMPLE}}{}{}".format(rt1,config["input_extension"])]
 if paired:
@@ -86,12 +89,13 @@ final_output = []
 #----------------------------------
 
 fastqc_input_fastq = input_data
-fastqc_output_done = "00-Fastqc/{{SAMPLE}}{}_fastqc.done".format(rt1)
-fastqc_wkdir = "00-Fastqc"
-fastqc_log = "00-Fastqc/logs/{{SAMPLE}}{}_fastqc_raw.log".format(rt1)
+fastqc_output_done = os.path.join(analysis_dir, "00-Fastqc/{{SAMPLE}}{}_fastqc.done".format(rt1))
+fastqc_wkdir = os.path.join(analysis_dir, "00-Fastqc")
+fastqc_log = os.path.join(analysis_dir, "00-Fastqc/logs/{{SAMPLE}}{}_fastqc_raw.log".format(rt1))
 final_output.extend(expand(fastqc_output_done, SAMPLE=samples))
 include: os.path.join(RULES, "fastqc.rules")
 
+
 #----------------------------------
 # remove adapters
 #----------------------------------
@@ -99,17 +103,17 @@ include: os.path.join(RULES, "fastqc.rules")
 if config["adapters"]["remove"] :
     adapter_tool = config["adapters"]["tool"]
     adapters_input_fastq = input_data
-    adapters_wkdir = "01-Trimming"
-    adapters_output = ["01-Trimming/{{SAMPLE}}{}_trim.fastq".format(rt1)]
+    adapters_wkdir = os.path.join(analysis_dir, "01-Trimming")
+    adapters_output = [os.path.join(analysis_dir, "01-Trimming/{{SAMPLE}}{}_trim.fastq".format(rt1))]
     if paired:
-        adapters_output += ["01-Trimming/{{SAMPLE}}{}_trim.fastq".format(rt2)]
+        adapters_output += [os.path.join(analysis_dir, "01-Trimming/{{SAMPLE}}{}_trim.fastq".format(rt2))]
 
     # Set parameters
     adapters_options = config["adapters"]["options"]
     adapters_mode = config["adapters"]["mode"]
     adapters_min  = config["adapters"]["m"]
     adapters_qual = config["adapters"]["quality"]
-    adapters_log = "01-Trimming/logs/{SAMPLE}_trim.txt"
+    adapters_log = os.path.join(analysis_dir, "01-Trimming/logs/{SAMPLE}_trim.txt")
     #final_output.extend(expand(adapters_output, SAMPLE=samples))
     if adapter_tool == "cutadapt" :
         include: os.path.join(RULES, "cutadapt.rules")
@@ -123,6 +127,21 @@ else:
     adapters_output = input_data
     
 
+   
+#-----------------------------------------
+# fastq_screen on samples
+#-----------------------------------------
+
+if config["fastq_screen"]["do"] :  
+    fastq_screen_input = adapters_output
+    fastq_screen_outdir = os.path.join(analysis_dir, "02-Mapping/Fastq-screen/{SAMPLE}")
+    fastq_screen_logs_err = os.path.join(analysis_dir, "02-Mapping/Fastq-screen/logs/{SAMPLE}_mapping.err")
+    fastq_screen_logs_out = os.path.join(analysis_dir, "02-Mapping/Fastq-screen/logs/{SAMPLE}_mapping.out")
+    final_output.extend(expand(fastq_screen_outdir, SAMPLE=samples))
+    include: os.path.join(RULES, "fastq_screen.rules")
+
+
+
 #-----------------------------------------
 # Estimate ribosomal rate in samples
 #-----------------------------------------
@@ -131,17 +150,21 @@ else:
 if config["genome"]["rRNA_mapping"] :
     sortmerna_input = adapters_output
     sortmerna_fasta = config["genome"]["ribo_fasta_file"]
-    sortmerna_outfile_rRNA = ["02-Mapping/Ribo/{{SAMPLE}}_rRNA{}.fastq".format(rt1)]
-    sortmerna_outfile_no_rRNA = ["02-Mapping/Ribo/{{SAMPLE}}_norRNA{}.fastq".format(rt1)]
+    sortmerna_outfile_rRNA = [os.path.join(analysis_dir, "02-Mapping/Ribo/{{SAMPLE}}_rRNA{}.fastq".format(rt1))]
+    sortmerna_outfile_no_rRNA = [os.path.join(analysis_dir, "02-Mapping/Ribo/{{SAMPLE}}_norRNA{}.fastq".format(rt1))]
     if paired:
-        sortmerna_outfile_rRNA += ["02-Mapping/Ribo/{{SAMPLE}}_rRNA{}.fastq".format(rt2)]
-        sortmerna_outfile_no_rRNA += ["02-Mapping/Ribo/{{SAMPLE}}_norRNA{}.fastq".format(rt2)]
-    sortmerna_logs_err = "02-Mapping/Ribo/logs/{SAMPLE}_mapping.err"
-    sortmerna_logs_out = "02-Mapping/Ribo/logs/{SAMPLE}_mapping.out"
+        sortmerna_outfile_rRNA += [os.path.join(analysis_dir, "02-Mapping/Ribo/{{SAMPLE}}_rRNA{}.fastq".format(rt2))]
+        sortmerna_outfile_no_rRNA += [os.path.join(analysis_dir, "02-Mapping/Ribo/{{SAMPLE}}_norRNA{}.fastq".format(rt2))]
+    sortmerna_logs_err = os.path.join(analysis_dir, "02-Mapping/Ribo/logs/{SAMPLE}_mapping.err")
+    sortmerna_logs_out = os.path.join(analysis_dir, "02-Mapping/Ribo/logs/{SAMPLE}_mapping.out")
     final_output.extend(expand(sortmerna_outfile_no_rRNA, SAMPLE=samples))
     include: os.path.join(RULES, "sortmerna.rules")
+    adapters_output = sortmerna_outfile_no_rRNA
+
+
+
+
 
-   
 #----------------------------------
 # genome gestion
 #----------------------------------
@@ -153,11 +176,28 @@ if config["genome"]["host_mapping"]:
 
 
 def mapping_index(wildcards):
+    if (wildcards.REF == config["genome"]["name"]):
+        if config["salmon"]["do"] and not config["genome"]["host_mapping"]:
+            return {"fasta": config["salmon"]["fasta"]}
+        else:
+            return {"fasta": config["genome"]["fasta_file"]}
+    elif (wildcards.REF == config["genome"]["host_name"]):
+        if config["salmon"]["do"]:
+            return {"fasta": config["salmon"]["fasta"]}
+        else:       
+            return {"fasta": config["genome"]["host_fasta_file"]}
+
+def bowtie2_mapping_index(wildcards):
     if (wildcards.REF == config["genome"]["name"]):
         return {"fasta": config["genome"]["fasta_file"]}
     elif (wildcards.REF == config["genome"]["host_name"]):
         return {"fasta": config["genome"]["host_fasta_file"]}
 
+def minimap2_mapping_index(wildcards):
+    if (wildcards.REF == config["genome"]["name"]):
+        return config["genome"]["fasta_file"]
+    elif (wildcards.REF == config["genome"]["host_name"]):
+        return config["genome"]["host_fasta_file"]
   
 def mapping_prefix(wildcards):
     if (wildcards.REF == config["genome"]["name"]):
@@ -168,9 +208,15 @@ def mapping_prefix(wildcards):
   
 def annot_index(wildcards):
     if (wildcards.REF == config["genome"]["name"]):
-        return {"gff_file": config["genome"]["gff_file"]}
+        if config["salmon"]["do"] and not config["genome"]["host_mapping"]:
+            return {"gff_file": config["salmon"]["fasta"]}
+        else:
+            return {"gff_file": config["genome"]["gff_file"]}
     elif (wildcards.REF == config["genome"]["host_name"]):
-        return {"gff_file": config["genome"]["host_gff_file"]}
+        if config["salmon"]["do"]:
+            return {"gff_file": config["salmon"]["fasta"]}
+        else:
+            return {"gff_file": config["genome"]["host_gff_file"]}
 
 
 #----------------------------------
@@ -183,11 +229,10 @@ if config["bowtie2_mapping"]["do"]:
     mapper += ["bowtie2"]
 
     # indexing for bowtie2
-    bowtie2_index_fasta = unpack(mapping_index)
-    bowtie2_index_log = "02-Mapping/{REF}/bowtie2/logs/bowtie2_{REF}_indexing.log"
+    bowtie2_index_fasta = unpack(bowtie2_mapping_index)
+    bowtie2_index_log = os.path.join(analysis_dir, "02-Mapping/{REF}/bowtie2/logs/bowtie2_{REF}_indexing.log")
     bowtie2_index_output_done = os.path.join(config["genome"]["genome_directory"], "{REF}/bowtie2/{REF}.1.bt2")
     bowtie2_index_output_prefix = os.path.join(config["genome"]["genome_directory"], "{REF}/bowtie2/{REF}")
-                   
     include: os.path.join(RULES, "bowtie2_index.rules")
 
 
@@ -195,11 +240,11 @@ if config["bowtie2_mapping"]["do"]:
     # Mapping step
     bowtie2_mapping_input = adapters_output
     bowtie2_mapping_index_done = bowtie2_index_output_done
-    bowtie2_mapping_sort = "02-Mapping/{REF}/bowtie2/{SAMPLE}_{REF}_sort.bam"
-    bowtie2_mapping_bam = "02-Mapping/{REF}/bowtie2/{SAMPLE}_{REF}.bam"
-    bowtie2_mapping_sortprefix = "02-Mapping/{REF}/bowtie2/{SAMPLE}_{REF}_sort"
-    bowtie2_mapping_logs_err = "02-Mapping/{REF}/bowtie2/logs/{SAMPLE}_{REF}_mapping.err"
-    bowtie2_mapping_logs_out = "02-Mapping/{REF}/bowtie2/logs/{SAMPLE}_{REF}_mapping.out"
+    bowtie2_mapping_sort = os.path.join(analysis_dir, "02-Mapping/{REF}/bowtie2/{SAMPLE}_{REF}_sort.bam")
+    bowtie2_mapping_bam = os.path.join(analysis_dir, "02-Mapping/{REF}/bowtie2/{SAMPLE}_{REF}.bam")
+    bowtie2_mapping_sortprefix = os.path.join(analysis_dir, "02-Mapping/{REF}/bowtie2/{SAMPLE}_{REF}_sort")
+    bowtie2_mapping_logs_err = os.path.join(analysis_dir, "02-Mapping/{REF}/bowtie2/logs/{SAMPLE}_{REF}_mapping.err")
+    bowtie2_mapping_logs_out = os.path.join(analysis_dir, "02-Mapping/{REF}/bowtie2/logs/{SAMPLE}_{REF}_mapping.out")
     bowtie2_mapping_prefix_index = bowtie2_index_output_prefix
     bowtie2_mapping_options =  config["bowtie2_mapping"]["options"]
     final_output.extend(expand(bowtie2_mapping_sort, SAMPLE=samples, REF=ref))
@@ -214,7 +259,7 @@ if config["star_mapping"]["do"]:
     mapper += ["STAR"]
     star_index_fasta = unpack(mapping_index)
     star_mapping_splice_file = unpack(annot_index)
-    star_index_log = "02-Mapping/{REF}/STAR/logs/STAR_{REF}_indexing.log"
+    star_index_log = os.path.join(analysis_dir, "02-Mapping/{REF}/STAR/logs/STAR_{REF}_indexing.log")
     star_index_output_done = os.path.join(config["genome"]["genome_directory"], "{REF}/STAR/SAindex")
     star_index_output_dir = os.path.join(config["genome"]["genome_directory"], "{REF}/STAR/")
  
@@ -226,15 +271,15 @@ if config["star_mapping"]["do"]:
     star_mapping_pass1_done = star_index_output_done
     star_mapping_pass1_index = star_index_output_dir
     if config["star_mapping"]["pass2"] == "none":
-        star_mapping_pass1_logs = "02-Mapping/{REF}/STAR/logs/{SAMPLE}_{REF}.out"
-        star_mapping_pass1_output_prefix =  "02-Mapping/{REF}/STAR/{SAMPLE}_{REF}_"
-        star_mapping_pass1_junctions = "02-Mapping/{REF}/STAR/{SAMPLE}_{REF}_SJ.out.tab"
-        star_mapping_pass1_bam =  "02-Mapping/{REF}/STAR/{SAMPLE}_{REF}_Aligned.sortedByCoord.out.bam"
+        star_mapping_pass1_logs = os.path.join(analysis_dir, "02-Mapping/{REF}/STAR/logs/{SAMPLE}_{REF}.out")
+        star_mapping_pass1_output_prefix =  os.path.join(analysis_dir, "02-Mapping/{REF}/STAR/{SAMPLE}_{REF}_")
+        star_mapping_pass1_junctions = os.path.join(analysis_dir, "02-Mapping/{REF}/STAR/{SAMPLE}_{REF}_SJ.out.tab")
+        star_mapping_pass1_bam =  os.path.join(analysis_dir, "02-Mapping/{REF}/STAR/{SAMPLE}_{REF}_Aligned.sortedByCoord.out.bam")
     else :
-        star_mapping_pass1_logs = "02-Mapping/{REF}/STAR/logs/{SAMPLE}_{REF}_init.out"
-        star_mapping_pass1_output_prefix =  "02-Mapping/{REF}/STAR/{SAMPLE}_{REF}_init_"
-        star_mapping_pass1_junctions = "02-Mapping/{REF}/STAR/{SAMPLE}_{REF}_init_SJ.out.tab"
-        star_mapping_pass1_bam =  "02-Mapping/{REF}/STAR/{SAMPLE}_{REF}_init_Aligned.sortedByCoord.out.bam"
+        star_mapping_pass1_logs = os.path.join(analysis_dir, "02-Mapping/{REF}/STAR/logs/{SAMPLE}_{REF}_init.out")
+        star_mapping_pass1_output_prefix =  os.path.join(analysis_dir, "02-Mapping/{REF}/STAR/{SAMPLE}_{REF}_init_")
+        star_mapping_pass1_junctions = os.path.join(analysis_dir, "02-Mapping/{REF}/STAR/{SAMPLE}_{REF}_init_SJ.out.tab")
+        star_mapping_pass1_bam =  os.path.join(analysis_dir, "02-Mapping/{REF}/STAR/{SAMPLE}_{REF}_init_Aligned.sortedByCoord.out.bam")
     star_mapping_pass1_read_groups = ""
     #final_output.extend(expand(star_mapping_pass1_junctions, SAMPLE=samples, REF=ref))    
     include: os.path.join(RULES, "star_mapping_pass1.rules")  
@@ -244,30 +289,50 @@ if config["star_mapping"]["do"]:
         star_mapping_pass2_input = adapters_output
         star_mapping_pass2_done = star_index_output_done
         star_mapping_pass2_index = star_index_output_dir
-        star_mapping_pass2_logs = "02-Mapping/{REF}/STAR/logs/{SAMPLE}_{REF}.out"
-        star_mapping_pass2_output_prefix =  "02-Mapping/{REF}/STAR/{SAMPLE}_{REF}_"
+        star_mapping_pass2_logs = os.path.join(analysis_dir, "02-Mapping/{REF}/STAR/logs/{SAMPLE}_{REF}.out")
+        star_mapping_pass2_output_prefix =  os.path.join(analysis_dir, "02-Mapping/{REF}/STAR/{SAMPLE}_{REF}_")
         if config["star_mapping"]["pass2"] == "by-sample":
-            star_mapping_pass2_junctions = "02-Mapping/{REF}/STAR/{SAMPLE}_{REF}_init_SJ.out.tab"
+            star_mapping_pass2_junctions = os.path.join(analysis_dir, "02-Mapping/{REF}/STAR/{SAMPLE}_{REF}_init_SJ.out.tab")
         elif config["star_mapping"]["pass2"] == "all-samples":
-            star_mapping_pass2_junctions = expand("02-Mapping/{{REF}}/STAR/{SAMPLE}_{{REF}}_init_SJ.out.tab", SAMPLE=samples)
+            star_mapping_pass2_junctions = expand(os.path.join(analysis_dir, "02-Mapping/{{REF}}/STAR/{SAMPLE}_{{REF}}_init_SJ.out.tab"), SAMPLE=samples)
         else:
             raise ValueError("Please provides a valid option to pass2 of STAR: must be by-sample, all-samples or none")
         star_mapping_pass2_bam = star_mapping_pass1_bam
         star_mapping_pass2_read_groups = "ID:{SAMPLE}"
-        star_mapping_pass2_sort = "02-Mapping/{REF}/STAR/{SAMPLE}_{REF}_Aligned.sortedByCoord.out.bam"
+        star_mapping_pass2_sort = os.path.join(analysis_dir, "02-Mapping/{REF}/STAR/{SAMPLE}_{REF}_Aligned.sortedByCoord.out.bam")
 
         final_output.extend(expand(star_mapping_pass2_sort, SAMPLE=samples, REF=ref))    
         include: os.path.join(RULES, "star_mapping_pass2.rules")    
   
+#----------------------------------
+# MINIMAP2 MAPPING
+#----------------------------------
+
+
+if config["minimap2"]["do"]: 
+    mapper += ["minimap2"]
+
+    minimap2_input = adapters_output
+    minimap2_genome = minimap2_mapping_index
+    minimap2_sort = os.path.join(analysis_dir, "02-Mapping/{REF}/minimap2/{SAMPLE}_{REF}_sort.bam")
+    minimap2_bam = os.path.join(analysis_dir, "02-Mapping/{REF}/minimap2/{SAMPLE}_{REF}.bam")
+    minimap2_logs_err = os.path.join(analysis_dir, "02-Mapping/{REF}/minimap2/logs/{SAMPLE}_{REF}_mapping.err")
+    minimap2_logs_out = os.path.join(analysis_dir, "02-Mapping/{REF}/minimap2/logs/{SAMPLE}_{REF}_mapping.out")
+    minimap2_options = config["minimap2"]["options"]
+    final_output.extend(expand(minimap2_sort, SAMPLE=samples, REF=ref))
+    include: os.path.join(RULES, "minimap2.rules")
+
 
 #----------------------------------
 # Mark duplicated reads
 #----------------------------------
 def output_mapping(wildcards):
     if (wildcards.MAP == "bowtie2"):
-        input = "02-Mapping/{REF}/{MAP}/{SAMPLE}_{REF}_sort.bam"
+        input = os.path.join(analysis_dir, "02-Mapping/{REF}/{MAP}/{SAMPLE}_{REF}_sort.bam")
     elif (wildcards.MAP == "STAR"):
-        input = "02-Mapping/{REF}/{MAP}/{SAMPLE}_{REF}_Aligned.sortedByCoord.out.bam"
+        input = os.path.join(analysis_dir, "02-Mapping/{REF}/{MAP}/{SAMPLE}_{REF}_Aligned.sortedByCoord.out.bam")
+    elif (wildcards.MAP == "minimap2"):
+        input = os.path.join(analysis_dir, "02-Mapping/{REF}/{MAP}/{SAMPLE}_{REF}_sort.bam")
     return(input)
 
 #if mapping on ribosomal RNA done, do not perform markDuplicates, counting or coverage
@@ -276,10 +341,10 @@ if "Ribo" in ref:
 
 if config["mark_duplicates"]["do"]:
     mark_duplicates_input = output_mapping
-    mark_duplicates_output = "02-Mapping/{REF}/{MAP}/{SAMPLE}_{REF}_sort_dedup.bam"
-    mark_duplicates_metrics = "02-Mapping/{REF}/{MAP}/{SAMPLE}_{REF}_sort_dedup.txt"
-    mark_duplicates_log_std = "02-Mapping/{REF}/{MAP}/logs/{SAMPLE}_{REF}_sort_dedup.out"
-    mark_duplicates_log_err = "02-Mapping/{REF}/{MAP}/logs/{SAMPLE}_{REF}_sort_dedup.err"
+    mark_duplicates_output = os.path.join(analysis_dir, "02-Mapping/{REF}/{MAP}/{SAMPLE}_{REF}_sort_dedup.bam")
+    mark_duplicates_metrics = os.path.join(analysis_dir, "02-Mapping/{REF}/{MAP}/{SAMPLE}_{REF}_sort_dedup.txt")
+    mark_duplicates_log_std = os.path.join(analysis_dir, "02-Mapping/{REF}/{MAP}/logs/{SAMPLE}_{REF}_sort_dedup.out")
+    mark_duplicates_log_err = os.path.join(analysis_dir, "02-Mapping/{REF}/{MAP}/logs/{SAMPLE}_{REF}_sort_dedup.err")
     mark_duplicates_tmpdir = config['tmpdir']
     final_output.extend(expand(mark_duplicates_output, SAMPLE=samples, REF=ref, MAP=mapper))
     include: os.path.join(RULES, "mark_duplicates.rules")
@@ -308,25 +373,44 @@ def counting_options(wildcards):
 
 if config["feature_counts"]["do"]: 
     if config["mark_duplicates"]["remove"]:
-        feature_counts_input = "02-Mapping/{REF}/{MAP}/{SAMPLE}_{REF}_sort_dedup.bam"
+        feature_counts_input = os.path.join(analysis_dir, "02-Mapping/{REF}/{MAP}/{SAMPLE}_{REF}_sort_dedup.bam")
     else:
         feature_counts_input = output_mapping
-    feature_counts_output_count = "03-Counting/{REF}/{MAP}/{SAMPLE}_{REF}_feature.out"
+    feature_counts_output_count = os.path.join(analysis_dir, "03-Counting/{REF}/{MAP}/{SAMPLE}_{REF}_feature.out")
     feature_counts_gff  = counting_gff
-    feature_counts_logs_err = "03-Counting/logs/{MAP}/{SAMPLE}_{REF}_feature.err"
-    feature_counts_logs_out = "03-Counting/logs/{MAP}/{SAMPLE}_{REF}_feature.out"
+    feature_counts_logs_err = os.path.join(analysis_dir, "03-Counting/logs/{MAP}/{SAMPLE}_{REF}_feature.err")
+    feature_counts_logs_out = os.path.join(analysis_dir, "03-Counting/logs/{MAP}/{SAMPLE}_{REF}_feature.out")
     feature_counts_options = counting_options
     final_output.extend(expand(feature_counts_output_count, SAMPLE=samples, REF=ref, MAP=mapper))
     include: os.path.join(RULES, "feature_counts.rules")
 
 
+
+#----------------------------------
+# Quantification with Salmon
+#----------------------------------
+
+if config["salmon"]["do"]: 
+        
+    #pseudo mapping
+    salmon_quant_bam = star_mapping_pass2_sort
+    salmon_quant_transcript = config["salmon"]["fasta"]
+    salmon_quant_output_dir = os.path.join(analysis_dir, "03-Counting/salmon/{SAMPLE}_{REF}")
+    salmon_quant_options = config["salmon"]["options"]
+    salmon_quant_log_err = os.path.join(analysis_dir, "03-Counting/salmon/logs/{SAMPLE}_{REF}_salmon.err")
+    salmon_quant_log_out = os.path.join(analysis_dir, "03-Counting/salmon/logs/{SAMPLE}_{REF}_salmon.out")
+    final_output.extend(expand(salmon_quant_output_dir, SAMPLE=samples, REF=ref))
+    include: os.path.join(RULES, "salmon_quant.rules")
+
+
+
 #----------------------------------
 # Samtools Flagstat
 #----------------------------------
 
 flagstat_input = output_mapping
-flagstat_logs = "02-Mapping/{REF}/{MAP}/logs/{SAMPLE}_{REF}.out"
-flagstat_output = "02-Mapping/{REF}/{MAP}/{SAMPLE}_{REF}_stats.out"
+flagstat_logs = os.path.join(analysis_dir, "02-Mapping/{REF}/{MAP}/logs/{SAMPLE}_{REF}.out")
+flagstat_output = os.path.join(analysis_dir, "02-Mapping/{REF}/{MAP}/{SAMPLE}_{REF}_stats.out")
 final_output.extend(expand(flagstat_output, SAMPLE=samples, REF=ref, MAP=mapper))    
 include: os.path.join(RULES, "flagstat.rules")  
 
@@ -336,32 +420,42 @@ include: os.path.join(RULES, "flagstat.rules")
 #----------------------------------
 if config["bamCoverage"]["do"]:
     bamCoverage_input = output_mapping
-    bamCoverage_logs = "04-Coverage/{REF}/{MAP}/logs/{SAMPLE}_{REF}.out"
-    bamCoverage_output = "04-Coverage/{REF}/{MAP}/{SAMPLE}_{REF}.bw"
+    bamCoverage_logs = os.path.join(analysis_dir, "04-Coverage/{REF}/{MAP}/logs/{SAMPLE}_{REF}.out")
+    bamCoverage_output = os.path.join(analysis_dir, "04-Coverage/{REF}/{MAP}/{SAMPLE}_{REF}.bw")
     bamCoverage_options = config['bamCoverage']['options']
     final_output.extend(expand(bamCoverage_output, SAMPLE=samples, REF=ref, MAP=mapper))    
     include: os.path.join(RULES, "bamCoverage.rules")  
 
+    if config["bamCoverage"]["igv_session"]:
+        igv_session_input = expand(bamCoverage_output, SAMPLE=samples, REF=ref, MAP=mapper)
+        igv_session_output = os.path.join(analysis_dir, "04-IGV/igv_session.xml")
+        igv_session_genome = ref
+        igv_session_wdir = os.path.join(analysis_dir, "04-IGV/")
+        igv_session_autoScale = "True"
+        igv_session_normalize = "False"
+        igv_session_log_out = os.path.join(analysis_dir, "04-IGV/logs/igv_session.out")
+        final_output.extend([igv_session_output])
+        include: os.path.join(RULES, "igv_session.rules")
 
 #----------------------------------
 # PseudoMapping with Kallisto
 #----------------------------------
 
-if config["pseudomapping"]["do"]: 
-    kallisto_index_fasta = config["pseudomapping"]["fasta"]
-    kallisto_index_output = (os.path.splitext(config["pseudomapping"]["fasta"])[0])+".idx"
-    kallisto_index_kmer = config["pseudomapping"]["kmer"]
-    kallisto_index_log = "02-Mapping/STAR/logs/Kallisto_indexing.log"
+if config["kallisto"]["do"]: 
+    kallisto_index_fasta = config["kallisto"]["fasta"]
+    kallisto_index_output = (os.path.splitext(config["kallisto"]["fasta"])[0])+".idx"
+    kallisto_index_kmer = config["kallisto"]["kmer"]
+    kallisto_index_log = os.path.join(analysis_dir, "02-Mapping/STAR/logs/Kallisto_indexing.log")
     include: os.path.join(RULES, "kallisto_index.rules")
 
         
     #pseudo mapping
     kallisto_quant_fastq = adapters_output
-    kallisto_quant_index = (os.path.splitext(config["pseudomapping"]["fasta"])[0])+".idx"
-    kallisto_quant_output_dir = "02-Mapping/Kallisto/{SAMPLE}"
-    kallisto_quant_options = config["pseudomapping"]["options"]
-    kallisto_quant_gtf = config["pseudomapping"]["gtf"]
-    kallisto_pseudo_log = "02-Mapping/Kallisto/logs/{SAMPLE}_pseudomap.log"
+    kallisto_quant_index = (os.path.splitext(config["kallisto"]["fasta"])[0])+".idx"
+    kallisto_quant_output_dir = os.path.join(analysis_dir, "02-Mapping/Kallisto/{SAMPLE}")
+    kallisto_quant_options = config["kallisto"]["options"]
+    kallisto_quant_gtf = config["kallisto"]["gtf"]
+    kallisto_pseudo_log = os.path.join(analysis_dir, "02-Mapping/Kallisto/logs/{SAMPLE}_kallisto.log")
     final_output.extend(expand(kallisto_quant_output_dir, SAMPLE=samples))
     include: os.path.join(RULES, "kallisto_quant.rules")
 
@@ -372,10 +466,10 @@ if config["pseudomapping"]["do"]:
 #----------------------------------
 multiqc_input = final_output
 multiqc_input_dir = "."
-multiqc_logs = "05-Multiqc/multiqc.log"
-multiqc_output = "05-Multiqc/multiqc_report.html"
+multiqc_logs = os.path.join(analysis_dir, "05-Multiqc/multiqc.log")
+multiqc_output = os.path.join(analysis_dir, "05-Multiqc/multiqc_report.html")
 multiqc_options = config['multiqc']['options'] + " -c config/multiqc_config.yaml" 
-multiqc_output_dir = "05-Multiqc"
+multiqc_output_dir = os.path.join(analysis_dir, "05-Multiqc")
 final_output = [multiqc_output]
 include: os.path.join(RULES, "multiqc.rules")
 
@@ -389,7 +483,7 @@ onsuccess:
     import os
     import glob
     import shutil
-    for file in glob.glob('02-Mapping/STAR/*/*init*'):
+    for file in glob.glob('02-Mapping/*/STAR/*init*'):
         if os.path.isfile(file):
             os.remove(file)
         elif os.path.isdir(file):
diff --git a/config/.gitkeep b/config/.gitkeep
old mode 100644
new mode 100755
diff --git a/config/TruSeq_Stranded_RNA.fa b/config/TruSeq_Stranded_RNA.fa
old mode 100644
new mode 100755
diff --git a/config/cluster_config.json b/config/cluster_config.json
old mode 100644
new mode 100755
index 37e5b79d5433a6c16449bdd83cc9ac472a1f2adf..1f32fdec1abca72d03552d5227e1f9f974ebde11
--- a/config/cluster_config.json
+++ b/config/cluster_config.json
@@ -38,6 +38,12 @@
 	{
 		"ram" : "60G"
 	},
+
+	"minimap2" :
+	{
+		"ram" : "30G"
+	},
+
 	"mark_duplicates":
 	{
 		"ram" : "30G"
diff --git a/config/config.yaml b/config/config.yaml
old mode 100644
new mode 100755
index cc168307a5c18145ab92c5f1743f02066270c065..56ed5b3e4c13fb8f3cfa58df2adcad4597d27e37
--- a/config/config.yaml
+++ b/config/config.yaml
@@ -27,13 +27,13 @@
 
 # Absolute path of directory where fastq are stored
 # could be a single directory or a list of directory (data/*)
-input_dir: /absolute/path/to/data
+input_dir: /path/to/your/data
 # How mate paires are written in fastq
 input_mate: '_R[12]'
 # filemame extension
 input_extension: '.fastq.gz'
-# directory where you want (not yet fonctional sorry)
-analysis_dir: .
+# directory where you want 
+analysis_dir: results
 # tmpdir: write tempory file on this directory (could be /tmp/ or "/pasteur/appa/scratch/LOGIN/")
 tmpdir: $MYSCRATCH
 
@@ -41,7 +41,7 @@ tmpdir: $MYSCRATCH
 #===============================================================================
 # Genome Section
 # Note that this pipeline is conceived to used one or more genome. 
-# Please always fill the four first lines.
+# Please always fill the four first lines.
 #
 # :Parameters:
 #
@@ -49,25 +49,25 @@ tmpdir: $MYSCRATCH
 # - name: name of prefix use in all output files from mapping [First Genome]
 # - fasta_file: path to Reference Genome in fasta format [First Genome]
 # - gff_file : path to annotation file  [First Genome]
-# - host_mapping: set to True if you want align reads also against another genome [Second Genome]
+# - host_mapping: set to yes if you want align reads also against another genome [Second Genome]
 # - host_name: name of prefix use in all output files from mapping related to [Second Genome]
 # - host_fasta_file: path related to another genome in fasta format [Second Genome]
 # - gff_file : path to annotation file [Second Genome]
-# - rRNA_mapping: Mapping on ribosomal RNA. If true, sortmeRNA is used to estimate ribosomal rate
+# - rRNA_mapping: Mapping on ribosomal RNA. If yes, sortmeRNA is used to estimate ribosomal rate
 # - ribo_fasta_file : path to ribosomal sequences in fasta format
 #===============================================================================
 
 
 genome:
     genome_directory: /pasteur/zeus/projets/p01/BioIT/Genomes
-    name: Rabies
-    fasta_file: /pasteur/zeus/projets/p01/BioIT/Genomes/Rabies/Rabies.fa
-    gff_file: /pasteur/zeus/projets/p01/BioIT/Genomes/Rabies/Rabies.gff
-    host_mapping: true
+    name: saccer3
+    fasta_file: /pasteur/zeus/projets/p01/BioIT/Genomes/saccer3/saccer3.fa
+    gff_file: /pasteur/zeus/projets/p01/BioIT/Genomes/saccer3/saccer3.gff
+    host_mapping: yes
     host_name: hg38
     host_fasta_file: /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38.fa
     host_gff_file: /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38.gff
-    rRNA_mapping: true
+    rRNA_mapping: yes
     ribo_fasta_file: /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38_rRNA.fa  
 
 #===============================================================================
@@ -82,6 +82,23 @@ fastqc:
     options: --nogroup
     threads: 4   
 
+
+#===============================================================================
+# Fastq_screen section
+#
+# :Parameters:
+#
+# - do: if unchecked, this rule is ignored
+# - conf: string with any valid FastQC options
+#===============================================================================
+
+fastq_screen:
+    do: yes
+    conf: /pasteur/zeus/projets/p01/BioIT/Genomes/fastq_screen_conf/fastq_screen.conf
+    threads: 4 
+
+
+
 #===============================================================================
 # Quality trimming and adapter removal
 #
@@ -177,12 +194,12 @@ minimap2:
 # - fasta: Fasta file for the kallisto index to be used for quantification
 # - gtf: GTF file for transcriptome information (required for --genomebam)
 # - kmer: k-mer (odd) length (default: 31, max value: 31)
-# - options: any options recognised by bowtie2 tool
+# - options: any options recognised by kallisto tool
 # - threads: number of threads to be used
 #===============================================================================
 
 
-pseudomapping:
+kallisto:
     do: no
     fasta: /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38_cDNA.fa
     gtf: /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38.gtf
@@ -190,24 +207,33 @@ pseudomapping:
     kmer: 31 
     threads: 12
 
+
 #===============================================================================
-# mark duplicates (picard-tools) allows to mark PCR duplicate in BAM files
+# Quantification with Salmon quant (only available with STAR mapping)
 #
 # :Parameters:
 #
 # - do: if unchecked, this rule is ignored
-# - remove: If true do not write duplicates to the output file instead of writing
-#       them with appropriate flags set.  Default value: no. 
+# - fasta: Fasta file for the kallisto index to be used for quantification
+# - gtf: GTF file for transcriptome information (required for --genomebam)
+# - libtype: the type of sequencing library from which the reads come
+# - options: any options recognised by salmon
 # - threads: number of threads to be used
+#
+#
 #===============================================================================
 
-mark_duplicates:
+
+salmon:
     do: yes
-    remove: no
-    threads: 4
+    fasta: /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38_cDNA.fa
+    options: ""
+    libtype: "A" 
+    threads: 12
 
 
-#############################################################################
+
+#===============================================================================
 # feature_counts used to count reads against features
 #
 # :Parameters:
@@ -216,15 +242,33 @@ mark_duplicates:
 # - options: options related to the first genome
 # - options_host : options related to the host genome
 # - threads: number of threads to be used
-#
+#===============================================================================
+
+
 feature_counts:
     do: yes
-    options: "-t gene -g ID -s 1 " ## if exon/CDS is used, put -O option
-    options_host: "-t exon -g gene_id -s 1 "
-    threads: 2
+    options: "-t gene -g ID -s 1 " 
+    options_host: "-t gene -g gene_id -s 1 "
+    threads: 8
 
+#===============================================================================
+# mark duplicates (picard-tools) allows to mark PCR duplicate in BAM files
+#
+# :Parameters:
+#
+# - do: if unchecked, this rule is ignored
+# - remove: If true do not write duplicates to the output file instead of writing
+#       them with appropriate flags set.  Default value: no. 
+# - threads: number of threads to be used
+#===============================================================================
+
+mark_duplicates:
+    do: no
+    remove: no
+    threads: 4
 
-#############################################################################
+
+#===============================================================================
 # bamCoverage from Deeptools
 #  see https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html
 #
@@ -235,11 +279,14 @@ feature_counts:
 #   see https://deeptools.readthedocs.io/en/latest/content/feature/effectiveGenomeSize.html
 #       for more information about effective Genome Size
 # - threads: number of threads to be used
+#===============================================================================
+
 
 bamCoverage:
-    do: no
+    do: yes
     options: "--filterRNAstrand forward --effectiveGenomeSize 120000 " 
     options_host: "--filterRNAstrand forward --effectiveGenomeSize 2913022398 " 
+    igv_session: yes
     threads: 4
 
 
@@ -254,4 +301,4 @@ bamCoverage:
 
 
 multiqc:
-    options: " -f -x 02-Mapping/*/*/*_init_* -x .snakemake"
+    options: " -f -x 02-Mapping/*/*/*init* -x .snakemake"
diff --git a/config/multiqc_config.yaml b/config/multiqc_config.yaml
old mode 100644
new mode 100755
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index d0a3d46ffe0cdf83bd975a66b7894333e10eecf2..65f3a51b3ef81915206b2f11f03bc856eeb6184c 100644
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+++ b/images/rulegraph.svg
@@ -1,835 +1,1048 @@
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-   inkscape:version="0.92.5 (2060ec1f9f, 2020-04-08)">
+   viewBox="0.00 0.00 860.00 476.00"
+   height="476pt"
+   width="860pt">
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+    <!-- 5&#45;&gt;10 -->
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+    <!-- 11 -->
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