rename adapters options

README.md

@@ -136,7 +136,7 @@ run it in NNCR using environment modules via
 
 - Genome information
 
-fill only the first lines relative to the first genome
+Fill only the four first lines relative to the first genome with your eukaryotic genome. No need to fill "host_" information when host_mapping is set to no : lines will be ignored by the pipeline. In any case, no need to comment a line in the config.yaml, it will broke the pipeline.
 
 ```
 genome:
@@ -163,8 +163,8 @@ adapters:
     alien_file: config/TruSeq_Stranded_RNA.fa
     m: 25
     mode: b
-    #options: -O 6 --trim-n --max-n 1 # for cutadapt
-    options: -k 10 -m 5 -p 80  # for alienTrimmer
+    options_cutadapt: -O 6 --trim-n --max-n 1 
+    options_alien: -k 10 -m 5 -p 80  
     quality: 30
     threads: 4
 
@@ -196,9 +196,10 @@ Other tools are set to 'no'
 
 
 Why counting with Salmon and not STAR ? some informations here :
-https://www.sciencedirect.com/science/article/pii/S2001037020303032
-https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0141910#pone-0141910-t001
-https://f1000research.com/articles/4-1521/v2
+
+- https://www.sciencedirect.com/science/article/pii/S2001037020303032
+- https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0141910#pone-0141910-t001
+- https://f1000research.com/articles/4-1521/v2
 
 
 
@@ -206,7 +207,7 @@ https://f1000research.com/articles/4-1521/v2
 
 - Genome information
 
-fill the genome section with pathogen and host genomes
+Fill the genome section with pathogen and host genomes (fasta and gff)
 
 ```
 genome:
@@ -233,8 +234,8 @@ adapters:
     alien_file: config/TruSeq_Stranded_RNA.fa
     m: 25
     mode: b
-    #options: -O 6 --trim-n --max-n 1 # for cutadapt
-    options: -k 10 -m 5 -p 80  # for alienTrimmer
+    options_cutadapt: -O 6 --trim-n --max-n 1 
+    options_alien: -k 10 -m 5 -p 80  
     quality: 30
     threads: 4
 
@@ -282,7 +283,8 @@ Other tools are set to 'no'
 
 - Genome information
 
-fill the genome section with bacteria information
+Fill only the four first lines relative to the first genome with your prokaryotic genome. No need to fill "host_" information when host_mapping is set to no : lines will be ignored by the pipeline. In any case, no need to comment a line in the config.yaml, it will broke the pipeline.
+
 
 ```
 genome:
@@ -309,8 +311,8 @@ adapters:
     alien_file: config/TruSeq_Stranded_RNA.fa
     m: 25
     mode: b
-    #options: -O 6 --trim-n --max-n 1 # for cutadapt
-    options: -k 10 -m 5 -p 80  # for alienTrimmer
+    options_cutadapt: -O 6 --trim-n --max-n 1 
+    options_alien: -k 10 -m 5 -p 80  
     quality: 30
     threads: 4
 

Snakefile

@@ -109,15 +109,16 @@ if config["adapters"]["remove"] :
         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 = os.path.join(analysis_dir, "01-Trimming/logs/{SAMPLE}_trim.txt")
     #final_output.extend(expand(adapters_output, SAMPLE=samples))
     if adapter_tool == "cutadapt" :
+        adapters_options = config["adapters"]["options_cutadapt"]
         include: os.path.join(RULES, "cutadapt.rules")
     elif adapter_tool == "alienTrimmer" :
+        adapters_options = config["adapters"]["options_alien"]
         include: os.path.join(RULES, "alienTrimmer.rules")
     else :
         raise ValueError("Please provides an implemented removal adapter tool: must be cutadapt or alienTrimer")

config/config.yaml

@@ -128,8 +128,8 @@ adapters:
     alien_file: config/TruSeq_Stranded_RNA.fa
     m: 25
     mode: b
-    #options: -O 6 --trim-n --max-n 1 # for cutadapt
-    options: -k 10 -m 5 -p 80  # for alienTrimmer
+    options_cutadapt: -O 6 --trim-n --max-n 1 
+    options_alien: -k 10 -m 5 -p 80  
     quality: 30
     threads: 4