Run command

Option 1: Without cloning the repo

nextflow run JD2112/TwistNext -r main \
    -profile singularity \
    --sample_sheet Sample_sheet_twist.csv \
    --genome_fasta /data/reference_genome/hg38/hg38.fa \ 
    --diff_meth_method edger \
    --outdir Results/TwistNext_edgeR 

Option 2: Clone the git repo

git clone https://github.com/JD2112/TwistNext.git
cd TwistNext

With the reference genome, --genome_fasta

nextflow run main.nf \
    -profile singularity \
    --sample_sheet Sample_sheet_twist.csv \
    --genome_fasta data/reference_genome/hg38/hg38.fa \ 
    --diff_meth_method edger \
    --outdir /mnt/SD3/test_twistNext_dagTest_edgeR 

With the bisulfite index, --bismark_index

nextflow run main.nf \
    -profile singularity \
    --sample_sheet Sample_sheet_twist.csv \
    --bismark_index /data/reference_genome/hg38/ \ 
    --diff_meth_method edger \
    --outdir /mnt/Results/test_twistNext_dagTest_edgeR 

Use --diff_meth_method methylkit to run MethylKit analysis.

Help

nextflow run main.nf --help --outdir .