[](https://www.nextflow.io/) [](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 !