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......@@ -159,10 +159,10 @@ The [config file](config/) defines a dictionary of configuration parameters and
| 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: rapidrun | absolute path of the rapidrun .tsv file | [readwrite_rapidrun_demultiplexing](https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/blob/master/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: 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: 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 |
......@@ -174,13 +174,13 @@ The [config file](config/) defines a dictionary of configuration parameters and
### 1. Settings
[01_settings/readwrite_rapidrun_demultiplexing.py](01_settings/readwrite_rapidrun_demultiplexing.py): write the demultiplex.csv file that the Snakefiles will read to define their wildcards.
[01_settings/readwrite_rapidrun_demultiplexing.py](https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/blob/master/01_settings/readwrite_rapidrun_demultiplexing.py): write the demultiplex.csv file that the Snakefiles will read to define their wildcards.
* inputs:
* [sample description .dat files](resources/test/sample_description): a table with 6 columns (plaque, plaque1, barcode, primer5, primer3, infos) and rows as a `plaque` element description. Each sample description file belong to a `marker` wildcard.
* [config.yaml](config/): see configuration step
* [rapidrun.tsv](resources/test/all_samples.tsv) : a table with 5 columns (plaque, run, sample, projet ,marker) and rows as `projet`/`marker`/`run`/`plaque`==`sample` element description.
* [sample description .dat files](https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/tree/master/resources/test/sample_description): a table with 6 columns (plaque, plaque1, barcode, primer5, primer3, infos) and rows as a `plaque` element description. Each sample description file belong to a `marker` wildcard.
* [config.yaml](https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/tree/master/config): see configuration step
* [rapidrun.tsv](https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/blob/master/resources/test/all_samples.tsv) : a table with 5 columns (plaque, run, sample, projet ,marker) and rows as `projet`/`marker`/`run`/`plaque`==`sample` element description.
* output:
* [results/01_settings/demultiplexing.csv](results/01_settings) : a dataframe with 14 columns (demultiplex, projet, marker, run, plaque, sample ,barcode5, barcode3 , primer5, primer3, min_f, min_r, lenBarcode5, lenBarcode3) and rows as `projet`/`marker`/`run`/`plaque`==`sample` element description.
* [results/01_settings/demultiplexing.csv](https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/tree/master/results/01_settings) : a dataframe with 14 columns (demultiplex, projet, marker, run, plaque, sample ,barcode5, barcode3 , primer5, primer3, min_f, min_r, lenBarcode5, lenBarcode3) and rows as `projet`/`marker`/`run`/`plaque`==`sample` element description.
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