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...@@ -159,17 +159,17 @@ The [config file](config/) defines a dictionary of configuration parameters and ...@@ -159,17 +159,17 @@ The [config file](config/) defines a dictionary of configuration parameters and
| parameters | descriptions | softwares | rules | default values | excepted type | | 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 | | 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: 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 | | 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 | | 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: 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 | | 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 | | 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_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 | 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 | | 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: 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 | | 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: singularity:
ednatools: /media/superdisk/utils/conteneurs/ednatools.simg ednatools: /media/superdisk/utils/conteneurs/ednatools.simg
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