├── .gitattributes ├── .github └── workflows │ └── ci.yml ├── .gitignore ├── LICENSE ├── NOTICE ├── README.md ├── bin └── gghist.R ├── data ├── denylist.bed ├── genome.fa ├── known_variants.vcf.gz └── reads │ ├── rep1_1.fq.gz │ ├── rep1_2.fq.gz │ ├── rep2_1.fq.gz │ └── rep2_2.fq.gz ├── docker ├── Dockerfile └── README.adoc ├── figures ├── workflow.ai └── workflow.png ├── main.nf ├── modules.nf ├── nextflow.config ├── scripts ├── 1a_prepareGenome.sh ├── 1b_prepare.vcf.file4pipeline.sh ├── 2_pipeline.RNAseq.SNVs.sh ├── 3_pipeline.RNAseq.SNVs.mergeReplicates.sh ├── 4_process.vcfs.sh ├── 5_AE_pipeline.knownSNPs.sh └── README.txt └── validate-ci.sh /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CRG-CNAG/CalliNGS-NF/HEAD/.gitattributes -------------------------------------------------------------------------------- /.github/workflows/ci.yml: 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