Reference.md

@@ -160,6 +160,7 @@ The [config file](config/) defines a dictionary of configuration parameters and
 | 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](https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/blob/master/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: nb_chunk     | number of chunks to scatter fastq files in order to parallelize illuminapairedend step to proceed large fastq files. 0 value means that fastq file scattering will not be performed | [fastqsplitter](https://fastqsplitter.readthedocs.io/en/stable/) | split_fastq | 4 | integer
 | 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