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# The wf-illumina-nf pipeline
This pipeline performes the QC of data from Illumina sequencers.
## How tu use it ?
The pipeline begin after the NGS_Illumina pipeline, which, at the end performes the demultiplexing of raw data. In the output directory of demultiplexing, five elements are needed :
- one fastq files folder per project
- the SampleSheet.csv
- the nextflow outputs folder
- the params.config file
- the fastqScreen configration file
An example of the params.config and fastqScreen are available in the assets folder.
Example of a basic command line the launch the pipeline is (from the nextflow folder) :
```bash
sbatch -J nf-illumina_BHNKY7DRX2_1 -p wflowq -t 3-00 --mem 5GB --wrap="module load bioinfo/Nextflow-v21.04.1; cd /home/sbsuser/work/data/NovaSeq/230116_A00318_0372_BHNKY7DRX2_Lane1_1673933427_10x/nextflow; nextflow run /work/sbsuser/test/jules/VisualStudioSources/wf-illumina-nf/main.nf -profile prod -ansi-log false"
```
NB : for the moment, the case of multi-projects lane is not managed !