Reference.md

@@ -171,44 +171,16 @@ The [config file](config/) defines a dictionary of configuration parameters and
 | assign_taxon: bdr: `marker`      | absolute path to the folder of `marker` reference database and prefix | [ecotag](https://pythonhosted.org/OBITools/scripts/ecotag.html?highlight=ecotag#module-ecotag) | assign_taxon | /workdir/reference_database/`marker`/embl_std | absolute path of a folder + prefix |
 | assign_taxon: fasta: `marker`    |  absolute path to the .fasta file of the `marker` reference database | [ecotag](https://pythonhosted.org/OBITools/scripts/ecotag.html?highlight=ecotag#module-ecotag) | assign_taxon | /workdir/reference_database/`marker`/db_embl_std.fasta | absolute path file |
 
-singularity:
-  ednatools: /media/superdisk/utils/conteneurs/ednatools.simg
-  obitools: /media/superdisk/utils/conteneurs/obitools.simg
-fichiers:
-  rapidrun: 01_infos/all_samples.tsv
-  folder_fastq: /media/superdisk/edna/donnees/test/tiny_malpelo-fakarava_rapidrun/
-  folder_refdb: /media/superdisk/edna/donnees/reference_database/ref141/
-  dat:
-    mamm: /media/superdisk/edna/donnees/test/tiny_malpelo-fakarava_rapidrun/Mamm.dat
-    teleo: /media/superdisk/edna/donnees/test/tiny_malpelo-fakarava_rapidrun/Teleo.dat
-    chond: /media/superdisk/edna/donnees/test/tiny_malpelo-fakarava_rapidrun/Chond.dat
-    vert: /media/superdisk/edna/donnees/test/tiny_malpelo-fakarava_rapidrun/Vert.dat
-blacklist:
-  projet:
-    - dummy_run
-  run:
-    - 180430_SN234_A_L001_AIMI-9
-    - 180504_SND405_A_L001_AIMI-10
-    - 180504_SND405_A_L002_AIMI-11
-illuminapairedend:
-  s_min: 40
-good_length_samples:
-  seq_count : 1
-  seq_length : 1
-clean_pcrerr_samples:
-  r : 0.05
-assign_taxon:
-  bdr:
-    mamm: /media/superdisk/edna/donnees/reference_database/reference_database_mamm/embl_std
-    teleo: /media/superdisk/edna/donnees/reference_database/reference_database_teleo/embl_std
-    chond: /media/superdisk/edna/donnees/reference_database/reference_database_chond/embl_std
-    vert: /media/superdisk/edna/donnees/reference_database/reference_database_vert/embl_std
-  fasta:
+
+### 1. Settings
+
+[01_settings/readwrite_rapidrun_demultiplexing.py](01_settings/readwrite_rapidrun_demultiplexing.py) : 
 
 
 
-### 1. Settings
 
+| WARNING: be careful to baz the quux before initializing the retro encabulator! |
+| --- |