README.md

[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A50.32.0-brightgreen.svg)](https://www.nextflow.io/)

[![pipeline status](https://forgemia.inra.fr/get-nextflow-ngl-bi/template-nf/badges/master/pipeline.svg)](https://forgemia.inra.fr/get-nextflow-ngl-bi/template-nf//-/commits/master)


# 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 -params-file ../params.yml"
```

Tha YAML parameter file must looks like :
```
inputdir: "/home/sbsuser/work/Nextflow/wf-illumina-nf/data_test/NovaSeq/211129_A00318_0259_AHNMTTDSX2_Lane1_1638345606_dna"
project: 'GwOAK_small'
is_multiplex: true
data_nature: "DNA"
pairedEnd: true
reference_genome: "/save/ng6/TODO/HiSeqIndexedGenomes/new_struct/Quercus_robur/genome/GCA_900291515.1/BWA/GCA_900291515.1_Q_robur_v1_genomic.fna"
addBankForConta: ""
run_name: "ContaComparison"
sequencer: "NovaSeq"
run_date: "2022"
machine_id: "NOVA"
fc_id: "HNMTTDSX2"
lane: "1"
```


NB : for the moment, the case of multi-projects lane is not managed !