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bravo-protocols

VWorks protocols and other files for the Agilent NGS Workstations at the Genomics facility at SciLifeLab.

charon

Database for IGN projects and samples, with RESTful interface. Built on top of Tornado and CouchDB.

dds_web

A cloud-based system for the delivery of data from SciLifeLab Facilities to their users (e.g. research group).

flowcell_parser

Collection of python scripts to parse Illumina (demux with bcl2fastq v2.17+) output

genologics

Python interface to the GenoLogics LIMS server via its REST API.

genomics-status

Tornado server for tracking samples at NGI Stockholm

irma-provision

Ansible playbooks for provisioning NGI pipeline and related sw

lims2db

lims_dashboard

miarka-provision

Ansible playbooks for provisioning NGI cluster Miarka

modules

Repository to host tool-specific module files for the Nextflow DSL2 community!

multiqc

Aggregate results from bioinformatics analyses across many samples into a single report.

multiqc_ngi

MultiQC plugin for the National Genomics Infrastructure in Stockholm, Sweden.

multiqc_testdata

Test data for MultiQC. See https://github.com/ewels/MultiQC

ngi_dashboards

SciLifeLab NGI Dashboard Code

ngi_pipeline

Code driving the production pipeline at SciLifeLab

ngi_reports

Code to generate reports for use by the NGI in SciLifeLab

ngipubs

Web tool to find and annotate NGI publications

ngisweden.se

Wordpress theme and plugins for ngisweden.se

orderportal

A portal for orders (a.k.a. requests, project applications) to a facility from its users.

piper

A genomics pipeline build on top of the GATK Queue framework

rosalind

scilifelab

Misc code snippets for Science For Life Laboratory

scilifelab_epps

A collection of Genologics Clarity LIMS EPPs used at Scilifelab.

standalone_scripts

Repository to store standalone scripts that do not belong to any bigger package or repository

statusdb

Python wrappers and methods to work with CouchDB's instance at NGI Stockholm

taca

Tool for the Automation of Cleanup and Analyses: tools for projects and data management at NGI Stockholm

taca-ngi-pipeline

A TACA plugin adding functionality relevant for the ngi_pipeline

tools

Python package with helper tools for the nf-core community.

userman

Simple user account handling system for use with web services. Built on top of Tornado and CouchDb.