genomic-medicine-sweden/NGPGlue

Small scripts and other similar NGP solutions of sensitive nature

NGPGlue Script Index

Small scripts and other similar NGP solutions

artic2external

Invocation

perl artic2external.pl 
--prefix "test_illumina"
--fastq_directory .github/data/fastqs/
--artic_outdir illumina_test --metadata covidMetadataTemplate.[json|csv]

• Flags prefix, fastq_directory and artic_outdir should match that of GMS-Artic invocation.

• Metadata can be generated using the GMS-uploader.

• Metadata can be provided as either json or csv, determined by the file-suffix.

• Output is written to same output folder as gms-artic, e.g. {artic_outdir}/UploadStage/{prefix}/[fohm,gisaid]

• Metadata format is defined by the template at: https://kise.sharepoint.com/teams/GRP_GenomicMedicineSweden/Delade%20dokument/AU%20Mikrobiologi/Bioinformatik/Pipeline%20SARS-CoV-2/covidMetadataTemplate.csv?d=we199e2b9e0bc4a068dbd56e989a4d90b&csf=1&web=1&e=gHdedC

• Output is written to same output folder as gms-artic, e.g. {artic_outdir}/UploadStage/{prefix}/[fohm,gisaid]

• Output FoHM directory has subdirectories with fastq-files using the name suggested by FOHM (symlinked to the original files), a file with extra information *komplettering.csv and a file with pangolin-classification *classification_format3.txt. The files have lab-id, region-id and date as prefixes.

• Output GISAID directory has a metadata file GISAIDsubmission.csv, and a fasta-file GISAIDsubmission.fasta containing all consensus-sequences connected to the metadata. The files have lab-id, region-id and date as prefixes.

split_gms-artic.sh

This script splits a folder of fastqs into multiple smaller folders. This is a quick fix to avoid the concurrency issue of starting GMC-Artic on several thousand samples located in a single directory.

Limitations

The script will currently only work for the illumina workflow. The nanopore workflow requires a different input.

json2csv.pl

Simple json to csv conversion script