Commit bd00b6ab authored by Laure QUINTRIC's avatar Laure QUINTRIC
Browse files

readme update

parent a5116640
......@@ -37,7 +37,7 @@ Final output files are names :
* frogs/samples.tar archive for frogs
## How to run (IF RUN OUTSIDE ABYSS-PIPELINE) ?
**extract.ini** : configuration file to edit
- **extract.ini** : configuration file to edit
* DIRECTORY : current directory of pipeline
* INPUT : path to the input directory containing the fastq.gz reads files of one marker for several samples.
* OUTPUT : path to output directory
......@@ -46,9 +46,9 @@ Final output files are names :
* SAMPLENAME : path to the csv file containing abyss and genoscope sample names
* TRIMREADS : set to True if you want to perform all abyss preprocessing (cutadapt, bbmap, renaming) (option : True/False)
**extract.sh** : script which will run extract.py on the configuration file **extract.ini**. Each samples (and its two "paired-end" files) will be parse separately.
**extract.py** : python script that will read extract.ini file and launch extractR1R2.pbs calculation or each sample. The check.pbs script is run at the end to verify that all files are created at the end of the process for each sample.
**extractR1R2.pbs** : pbs script that will run extractR1R2.py which will execute the steps presented above (cutadapt, renaming files and reads, bbmap repair...)
- **extract.sh** : script which will run extract.py on the configuration file **extract.ini**. Each samples (and its two "paired-end" files) will be parse separately.
- **extract.py** : python script that will read extract.ini file and launch extractR1R2.pbs calculation or each sample. The check.pbs script is run at the end to verify that all files are created at the end of the process for each sample.
- **extractR1R2.pbs** : pbs script that will run extractR1R2.py which will execute the steps presented above (cutadapt, renaming files and reads, bbmap repair...)
```bash
./extract.sh
......
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