Reference.md

@@ -169,10 +169,62 @@ Summary, inputs, outputs of scripts. The scripts are ordered by steps
 5. Taxonomic assignment
 
 
-### 0 Configuration
-
-
-### 1 Settings
+### 0. Configuration
+
+The [config file](config/) defines a dictionary of configuration parameters and their values. These values will be used by the workflows.
+
+| parameters | descriptions | softwares | rules | default values | excepted type |
+|------------|--------------|-----------|-------|-----------|--------------------|
+| singularity                    | absolute path of singularity container file [![https://www.singularity-hub.org/static/simg/hosted-singularity--hub-%23e32929.svg](https://www.singularity-hub.org/static/img/hosted-singularity--hub-%23e32929.svg)](https://singularity-hub.org/collections/2878) | [singularity](https://singularity.lbl.gov/) | every rules need this container to work | /workdir/conteneur/obitools.simg | absolute path file |
+| fichiers/rapidrun              | absolute path of the rapidrun .tsv file | [readwrite_rapidrun_demultiplexing](01_settings/readwrite_rapidrun_demultiplexing.py) | settings | resources/test/all_samples.tsv | absolute path file |
+| fichiers/folder_fastq          | absolute path of a folder which contains pairend-end raw reads .fastq.gz |  [illuminapairedend](https://pythonhosted.org/OBITools/scripts/illuminapairedend.html?highlight=illumina#module-illuminapairedend) | illuminapairedend | /workdir/ngs/ | absolute path folder |
+| dat/`marker`                   | absolute path of `marker` sample description .dat file | [ngsfilter](https://pythonhosted.org/OBITools/scripts/ngsfilter.html) | assign_sequences | resources/test/sample_description/`marker`.dat | dictionnary `marker`: absolute path of file |
+| blacklist/projet               | list of `projet` to exclude from the analysis | [readwrite_rapidrun_demultiplexing](01_settings/readwrite_rapidrun_demultiplexing.py) | settings | dummy_projet | `projet` wildcards value |
+| blacklist/run                  list of `run` to exclude from the analysis | [readwrite_rapidrun_demultiplexing](01_settings/readwrite_rapidrun_demultiplexing.py) | settings | dummy_projet | `run` wildcards value |
+| illuminapairedend/s_min        | score for keeping alignment. If the alignment score is below this threshold both the sequences are  just  concatenated. The mode attribute is set to the value joined | [illuminapairedend](https://pythonhosted.org/OBITools/scripts/illuminapairedend.html?highlight=illumina#module-illuminapairedend) | illuminapairedend | 40 | integer |
+| good_length_samples/seq_count  |  minimum number of copy for keeping a sequence | [obigrep](https://pythonhosted.org/OBITools/scripts/obigrep.html?highlight=obigrep#module-obigrep) | good_length_samples | 1 | integer |
+| good_length_samples/seq_length | minimum length for keeping a sequence | [obigrep](https://pythonhosted.org/OBITools/scripts/obigrep.html?highlight=obigrep#module-obigrep) | good_length_samples | 23 | integer
+| clean_pcrerr_samples/r         | threshold ratio between counts  (rare/abundant  counts)  of  two sequence records  so that the less abundant one is a variant of the more abundant | [obiclean](https://pythonhosted.org/OBITools/scripts/obiclean.html?highlight=obiclean#module-obiclean) | clean_pcrerr_samples | 0.05 | float |
+| 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