| ... | ... | @@ -180,7 +180,7 @@ The [config file](config/) defines a dictionary of configuration parameters and |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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
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