refactor(config): add a config file template

config/config_template.yaml

+format: RAPIDRUN                #or CLASSIC (required = TRUE)
+resources:
+  job: 8
+singularity:
+  ednatools:                    #path to ednatools.simg singularity image (required = FALSE)
+  obitools:                     #path to obitools.simg singularity image (required = FALSE)
+fichiers:
+  rapidrun:                     #path to all_samples.csv (required = TRUE if format = RAPIDRUN)
+  folder_fastq:                 #path to fastq files (reuqired = TRUE)
+  dat:
+    mamm:                       #path to Mamm.dat
+    teleo:                      #path to Teleo.dat
+    chond:                      #path to Chond.dat
+    vert:                       #path to Vert.dat
+blacklist:                      #blacklisted projects/run to exclude from the analysis (default = dummy_run)
+projet:
+    - dummy_run
+  run:
+    - dummy_run
+reference:                      #path to ecoPCR taxonomy Databases and to fasta file containing reference sequences
+  mamm:
+    prefix: embl_std
+    folder: resources/test/test_rapidrun_data/bdr/reference_database_mamm/
+    fasta: resources/test/test_rapidrun_data/bdr/reference_database_mamm/db_embl_std.fasta
+  teleo: 
+    prefix: embl_std
+    folder: resources/test/test_rapidrun_data/bdr/reference_database_teleo/
+    fasta: resources/test/test_rapidrun_data/bdr/reference_database_teleo/db_embl_std.fasta
+  chond:
+    prefix: embl_std
+    folder: resources/test/test_rapidrun_data/bdr/reference_database_chond/
+    fasta: resources/test/test_rapidrun_data/bdr/reference_database_chond/db_embl_std.fasta
+  vert:
+    prefix: embl_std
+    folder: resources/test/test_rapidrun_data/bdr/reference_database_vert/
+    fasta: resources/test/test_rapidrun_data/bdr/reference_database_vert/db_embl_std.fasta
+custom_baseref: FALSE           #use custom reference database (required = TRUE, default = FALSE, type = boolean)
+custom_ref:                     #(required = FALSE if custom_baseref = FALSE)
+  marker:
+    taxonomy_folder:            #path to marker custom taxonomy
+    fasta:                      #path to marker custom fasta
+fastqc: False                   #run control quality (required = TRUE, default = FALSE, type = boolean)
+merge_fastq:
+  encoding: 33                  #VSEARCH, FASTQ output quality score ASCII base char (required = TRUE, default = 33)
+merging:
+  vsearch:
+    cores: 8                    #VSEARCH, number of threads to use, zero for all cores (required = TRUE, default = 8)
+demultiplexing:
+  maxLen: 120                   #Cutadapt, Discard reads longer than LEN (required = TRUE, default = 120, type = int)
+  minLen: 20                    #Cutadapt, Discard reads shorter than LEN (required = TRUE, default = 20, type = int)
+  job: 4                        #Cutadapt, Number of CPU cores to use. Use 0 to auto-detect (required = TRUE, default = 4)
+clustering:
+  swarm:
+    cores: 8                    #Swarm, number of threads to use (required = TRUE, default = 8)
+assignment:
+  ecotag:
+    minIdentity: 0.0            #minimum identity to consider (required = TRUE, default = 0.0, type = int)