User information

Welcome to the gms-artic wiki!

How to run the pipeline in ngp server

1. Upload data via sftp or rsync to

/gms-storage-aws/TEST/midnight/<sample_name> or
/gms-storage-aws/TEST/artic/<sample_name>* or 
/gms-storage-aws/TEST/illumina/<sample_name>

*needs to change config files. See below

2. Data file structure

for nanopore analysis (default is "midnight")

    sample_name
         |___ fast5_pass/
         |___ fastq_pass/
         |___ sequencing_summary.txt
         |___ meta_data.csv

for illumina analysis

    sample_name     
         |___ fastq/
         |___ meta_data.csv

3. Manual running of analysis pipeline (or Local computer)

Run Illumina pipeline

$ nextflow run main.nf -profile singularity,sge \
    --illumina --prefix "test_illumina"     \
    --directory .github/data/fastqs/    \
    --outdir illumina_test

Run Nanopore Pipeline PLEASE NOTE: Deafult is "midnight" protocol

$ nextflow run main.nf -profile singularity \
    --nanopolish --prefix "midnight" \
    --basecalled_fastq /home/test/fastq_pass/ \
    --fast5_pass /home/test/fast5_pass/ \
    --sequencing_summary /home/test/sequencing_summary_FAP82331_657703c9.txt \
    --scheme-directory primer_schemes/midnight/nCoV-2019/V1/ \
    --outdir /home/test/midnight_test -with-report midnight

PLEASE NOTE: To run the artic pipeline, please change the nanopore.config 'min_length' (default = 400) and 'max_length' (default = 700)

$ nextflow run main.nf -profile singularity,sge \
    --nanopolish --prefix "test_nanopore" \
    --basecalled_fastq .github/data/nanopore/20200311_1427_X1_FAK72834_a3787181/fastq_pass/ \
    --fast5_pass .github/data/nanopore/20200311_1427_X1_FAK72834_a3787181/fast5_pass/ \
    --sequencing_summary .github/data/nanopore/20200311_1427_X1_FAK72834_a3787181/sequencing_summary_FAK72834_298b7829.txt \
    --outdir nanopore_test

How the pipeline works