Midnighter/nextflow-utility-services

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Groovy
License
MIT License
Created over 1 year ago
Updated over 1 year ago

Midnighter/nextflow-utility-services

Midnighter

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A collection of Groovy classes that provide utility services to nextflow pipelines.

structurizr-python

A Python 3 port of Simon Brown's Structurizr diagrams-as-code architecture description tool.

nextflow-gotchas

A collection of unexpected challenges and learnings with nextflow and nf-core.

fastapi-mount

A minimal application for prototyping mounting the main FastAPI at a sub path.

errorpages-demo

A Docker stack that demonstrates different desirable behaviour of the traefik errors middleware. Please read the accompanying post.

BRENDA-Parser

Classes to parse the BRENDA database.

fastapi-base

A base Docker image for microservices using FastAPI. The Docker image environment is based on Alpine Linux or Debian.

Notebooks-Launcher

script to handle setting up, launching, and shutting down of ipython notebook instances per user.

jinja2-ospath

A tiny Jinja2 extension that introduces dirname and basename as template filters.

cookiecutter-python-package

A complete Python package cookiecutter template with lots of bells and whistles.

dependency-info

Retrieve and print Python package dependencies.

metanetx-sdk

Parse and process information from MetaNetX for MIRIAM compatibility using the Identifiers.org registries.

tyche

Randomly sub-sample sequencing reads to a specified coverage or number of bases.

jupyter_presentation

Material and notebooks for an interactive Jupyter presentation.

Jupyter Notebook

pymetabolism

handling of metabolic models for FBA, graph theory, and model io.

x-grumpy

A Docker image that can be run with x11docker in order to access the ScrumPy GUI without hassle.

nf-core-adr

Structurizr documentation of nf-core

pip-compile

A minimal Docker image that provides a Python environment with pip-tools in order to lock requirements files.

Everyday-Utilities

a collection of classes and functions for various non-project related purposes

cookiecutter-nf-plugin

A cookiecutter template for creating nextflow plugins.

PolymorphicCpp

Classes and functions demonstrating some of the tricky polymorphic behaviour of C++

pyorganism

a unified framework for analysing organisational principles in living organisms

FROG

Analysis of 50 metabolic models using the opencobra/jeweler pipeline.

nf-join-map

Demonstrate problems with merging channels using a map as the key to merge by.

nf-file-utils

Query files for their type and compression state.

travis-release-notes

Test repository for the improved Travis CI file-based release notes.

help.github.com

GitHub help guides

plasmid-verification

Semi-automated plasmid sequence verification.

kraken2-bracken-test-db

Temporary place to host the kraken2 & Bracken database construction pipeline.

visual-merge

Visualize package hierarchies and allow for links between different hierarchies.

Jupyter Notebook

metanetx-assets

Transform MetaNetX components information and load them into SQL storage.

python-conda-travis

Template for testing Python packages on Travis-CI using Miniconda.

MfinderWrapper

A python wrapper class for the mfinder C tool.

wikidata-analysis

Simple query to table conversion and language analysis.

Jupyter Notebook

meetup-ipyparallel

Material for the ipyparallel presentation at the Python Users Berlin meetup Oct 2016.

Jupyter Notebook