Commit 3395e4ce authored by Laure QUINTRIC's avatar Laure QUINTRIC
Browse files

update readme

parent 05a08ea2
......@@ -45,14 +45,15 @@ Final output files are names :
- 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.
- **extractR1R2.pbs** : pbs script that will run extractR1R2.py which will execute the steps presented above (cutadapt, renaming files and reads, bbmap repair...)
- **extractR1R2.pbs** : pbs script that will run extractR1R2.py which will execute the steps presented above (cutadapt, bbmap repair...)
```bash
./extract.sh
```
(c) 2020 - Ifremer
......@@ -2,8 +2,6 @@
[common]
#Do we process trimreads ?
trimreads = %(trim)s
#Do we only rename files with abyss sample names ?
rename = %(renameonly)s
#Below configuration is optimized to use abyss-preprocessing inside abyss-pipeline
#if run alone, see the alternative configuration in the comments
directory = %(main_dir)s/thirdparty/abyss-preprocessing
......@@ -19,5 +17,3 @@ indir = %(input_dir)s
#output directory with processed reads
output = %(ligation_preprocess_dir)s
#if run alone : ouput=PATH_TO_OUTPUT_DIRECTORY
#correspondance between genoscope and abyss names
samplename = %(correspondance_file)s
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