Merge pull request #41 from 3d-omics/ci

chore: update README

README.md

@@ -1,40 +1,44 @@
-# Snakemake workflow: `Bioinfo_Macro_Host_Genomics`
-
-[![Snakemake](https://img.shields.io/badge/snakemake-≥6.3.0-brightgreen.svg)](https://snakemake.github.io)
-[![GitHub actions status](https://github.com/3d-omics/Bioinfo_Macro_Host_Genomics/workflows/Tests/badge.svg?branch=main)](https://github.com/3d-omics/Bioinfo_Macro_Host_Genomics/actions?query=branch%3Amain+workflow%3ATests)
+# Snakemake workflow: `hg_genotype`
 
+[![Snakemake](https://img.shields.io/badge/snakemake-≥8-brightgreen.svg)](https://snakemake.github.io)
+[![Tests](https://github.com/3d-omics/hg_genotype/actions/workflows/main.yml/badge.svg)](https://github.com/3d-omics/hg_genotype/actions/workflows/main.yml)
 
 A Snakemake workflow for  Short Variant Discovery in Host Genomes
 
 
 ## Usage
 
 - Test that it works:
-  - Make sure you have installed snakemake, samtools and bcftools. Either
-    - install them with conda/mamba :`conda install -c bioconda samtools bcftools`).
-    - or create an environment (`conda create -n 3dohg -c bioconda snakemake samtools bcftools`), and activate it (`conda activate 3dohg`)
-  - Generate mock data with `bash workflow/scripts/generate_mock_data.sh`
-  - Run the pipeline: `snakemake --use-conda --jobs 8 all`. It will download all the necesary software through conda. It should take less than 5 minutes.
+  - Make sure you have installed `snakemake>=8`
+  - Run the pipeline: `snakemake --use-conda --profile profile/default --jobs 100`. It will download all the necesary software through conda. It should take less than 5 minutes.
 
 - Run it with your own data:
   - Edit `config/samples.tsv` and add your samples and where are they located.
   - Edit `config/features.tsv` with information regarding the reference you are using.
-  - Run the pipeline: `snakemake --use-conda --jobs 8 all`.
-  - (slurm users): `./run_slurm`
+  - Run the pipeline: `snakemake --use-conda --profile profile/default --jobs 8 all`.
+  - If you are in a cluster with slurm, add `--executor slurm`.
 
 ## Features
 
-- FASTQ processing with [`fastp`](https://github.com/OpenGene/fastp)
-- Mapping with [`bowtie2`](https://github.com/BenLangmead/bowtie2)
-- SAM/BAM/CRAM processing with [`samtools`](https://github.com/samtools/samtools) and [`picard`](https://github.com/broadinstitute/picard)
-- Sample swap detection with [`gtcheck`](https://github.com/samtools/bcftools)
-- SNP calling with [`GATK4`](https://github.com/broadinstitute/gatk)
-- SNP annotation with [`SNPEff`](https://github.com/pcingola/SnpEff)
+- FASTQ processing with `fastp`.
+- Mapping with `bwa-mem2`
+- SAM/BAM/CRAM processing with `samtools` and `GATK`.
+- SNP calling with `GATK4`.
+- SNP annotation with `SNPEff` and `VEP`
+- Sample swap detection with `somalier`.
+- Reporting with `MultiQC`.
 
 ## DAG
 
-![host_genomics_pipeline](./rulegraph.svg?raw=true)
+![host_genomics_pipeline](./schema.svg?raw=true)
 
 ## References
 
-TBA
+- [`fastp`](https://github.com/OpenGene/fastp)
+- [`bwa-mem2`](https://github.com/bwa-mem2/bwa-mem2)
+- [`samtools`](https://github.com/samtools/samtools)
+- [`GATK`](https://github.com/broadinstitute/gatk)
+- [`SNPEff`](https://github.com/pcingola/SnpEff)
+- [`VEP`](https://github.com/Ensembl/ensembl-vep)
+- [`somalier`](https://github.com/brentp/somalier)
+- [`MultiQC`](https://github.com/MultiQC/MultiQC)