Commit 05a08ea2 authored by Laure QUINTRIC's avatar Laure QUINTRIC
Browse files

readme update

parent bd00b6ab
......@@ -38,13 +38,12 @@ Final output files are names :
## How to run (IF RUN OUTSIDE ABYSS-PIPELINE) ?
- **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
* PROPERTIES : path to file containing forward and reverse primers for different markers
* BARCODE : name of the marker (ie : 18S-V1) (this marker must be listed in the PROPERTIES file)
* 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)
- 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
- PROPERTIES : path to file containing forward and reverse primers for different markers
- BARCODE : name of the marker (ie : 18S-V1) (this marker must be listed in the PROPERTIES file)
- TRIMREADS : set to True if you want to perform all abyss preprocessing (cutadapt, bbmap) (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.
......@@ -54,6 +53,6 @@ Final output files are names :
./extract.sh
```
(c) 2018 - Ifremer
(c) 2020 - Ifremer
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