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ansible-ci-test

ansible.bactocap

Ansible playbook for setting up dependencies for bactocap nextflow pipeline

ansible.bio_software

Ansible playbook for installing bioinformatics workflow and package managers

ansible.nextflow-container

Ansible playbook for installing Nextflow, Docker and SingularityCE. Tested using GitHub Actions.

autodatabase

automated kraken database build using nextflow DSL2

bit107-nextflow-solution

Solution to BIT107 nextflow tutorial

catwalk

chipseq-window-extract

Extracts chip-seq windows from reference chromosomes

climb-workshop-ansible

containerci-test

Testing automated Docker Hub and Singularity Hub builds

dockerfile.extract-core-genome

Dockerfile for the extract_core_genome.py script from LS-BSR

dockerfiles

Various Dockerfiles for bioinformatics, machine learning & NLP

docs

ena-fastq-fetch

Query the ENA for different types of data and bulk download

findneighbour

A server side application determining bacterial relatedness

findneighbour2

Compares large numbers of bacterial sequences

findneighbour3

Bacterial relatedness server, supporting sequence clustering & mixture detection

findneighbour4

A server delivering large scale, incrementable, bacterial relatedness monitoring

hadolint

Dockerfile linter, validate inline bash, written in Haskell

inimotif

inimotif-py

IniMotif in python

kraken-fastedit

Edits the sequence ID headers in FASTA files for building custom databases with kraken

kraken-report-scraper

Collate information from multiple kraken report files into one csv

kubeyaml

kubernetes yaml templates

lingpipe-templates

Templates for Named Entity Recognition (NER) using lingpipe

metahood

Snakemake Assembly pipeline

minos

Variant call adjudication

modules

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

nf-tower

Nextflow Tower system

nlp-bio-tools

Collection of dockerized apps for text mining, NLP, and machine learning classification of biomedical pdfs