Useful information

GMS-artic (ncov2019-artic-nf)

A nextflow pipeline with a GMS touch for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics).

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Major changes

• The illumina and nanopore tracks automatically run pangolin

gms-artic in ngp-gms

1. login to the system

ssh [email protected]
password
$

NOTE: sge process is not supported on the /gms-storage-aws/, so need to run the pipeline locally from /home

Things to consider before running the pipeline

1. Update the Singularity container once in a month.
2. Pangolin version is updating almost every month/twice per month.
3. For different nanopore pipelines, need to use different primers; primer-schemes are designed as per Nanopore protocol, need to choose the right one, before executing the run, --scheme-directory primer_schemes/[artic/midnight/eden]/nCoV-2019/[Version number]/
4. Separate Pangolin Singularity container required for the Nanopore analysis. Need to update the container regularly.

https://hub.docker.com/r/staphb/pangolin/tags?page=1&ordering=last_updated

5. Available Containers A. Cloud - i. Singularity - Illumina, Nanopore, Pangolin

   singularity pull library://jd2112/gms-artic-illumina/gms-artic-illumina.sif:latest
   singularity pull library://jd2112/gms-artic-illumina/gms-artic-nanopore.sif:latest
   singularity pull library://jd2112/gms-artic-illumina/pangolin:latest
   

   ii. Docker - Illumina, Nanopore, Pangolin

   docker pull jd21/gms-artic_illumina:latest
   docker pull jd21/gms-artic_nanopore:latest
   docker pull jd21/pangolin:latest
   

   B. Local iii.Singularity iv. Conda

2. Run Illumina pipeline

$ [your home]
$ cp /gms-storage-aws/gms-artic/ .
$ nextflow run main.nf -profile singularity,sge \
    --illumina --prefix "test_illumina"     \
    --directory .github/data/fastqs/    \
    --outdir illumina_test

3. Run Nanopore Pipeline

$ [your home]
$ cp /gms-storage-aws/gms-artic/ .
$ 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 \
    --scheme-directory primer_schemes/midnight/nCoV-2019/V1/ \
    --outdir nanopore_test

Other information

NOTES

INSTRUCTIONS TO DATA UPLOADER

Upload SAMPLE_FILES to the SAMPLE_DIRECTORY/
Requires -
i. For Illumina: illumina/<SAMPLE_NAME>
ii. For Nanopore
a. artic: artic/<SAMPLE_NAME>
b. midnight: midnight/<SAMPLE_NAME>
The result directory will contains $SAMPLE_NAME_Results_$date
e.g., SAMPLE_NAME = SRR001
The result directory name: SRR001_Results_2021-07-21
The SAMPLE files will be copied to another DIRECTORY
The SAMPLE_FILES will be removed from the SAMPLE_DIRECTORY/
Update Singularity containers

monthly build new containers
check for updates. important info: to run pipeline after downloading the latest from git, check files permission in bin/ folder.

Running autoloader to check new incoming data and metadata file

./autoloader.py

The program will continuously check the folder /gms-storage-aws/TEST/ for addition/deletion of data inside the folder