container | absolute path of singularity container file `obitools.simg` | [singularity](https://singularity.lbl.gov/) | every rules need this container to work | /workdir/obitools.simg | absolute path of `simg` file
container | absolute path of singularity container file `obitools.simg` | [singularity](https://singularity.lbl.gov/) | every rules need this container to work | /workdir/conteneur/obitools.simg | absolute path of `simg` file
fastqFolderPath | absolute path of a folder which contains pairend-end raw reads `.fastq.gz` files and the sample description `.dat` files. | [illuminapairedend](https://pythonhosted.org/OBITools/scripts/illuminapairedend.html?highlight=illumina#module-illuminapairedend), [ngsfilter](https://pythonhosted.org/OBITools/scripts/ngsfilter.html) | illuminapairedend, assign_sequences | /workdir/edna_miseq_rawdata/ | absolute path of a folder
fastqFiles | list of wildcard `{run}` where `{run}` is the name of the sequencing run | [illuminapairedend](https://pythonhosted.org/OBITools/scripts/illuminapairedend.html?highlight=illumina#module-illuminapairedend) | illuminapairedend | seqrunA, seqrunB | list of strings
barcodeFiles | a dictionary with `{run}` as key and associated sample description file as value | [ngsfilter](https://pythonhosted.org/OBITools/scripts/ngsfilter.html) | assign_sequences | {seqrunA : sample_description1.dat, seqrunB : sample_description2.dat} | dictionary
