Discover Midnighter/errorpages-demo Open Source project

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

nextflow-gotchas

Shell

fastapi-mount

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

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

nextflow-utility-services

Classes to parse the BRENDA database.

BRENDA-Parser

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

fastapi-base

Shell

Notebooks-Launcher

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

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

jinja2-ospath

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

cookiecutter-python-package

Retrieve and print Python package dependencies.

dependency-info

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

tyche

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

metanetx-sdk

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

pymetabolism

Material and notebooks for an interactive Jupyter presentation.

jupyter_presentation

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

x-grumpy

Makefile

nf-core-adr

Structurizr documentation of nf-core

ASL

cookiecutter-nf-plugin

A cookiecutter template for creating nextflow plugins.

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

Everyday-Utilities

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

pip-compile

Dockerfile

PolymorphicCpp

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

C++

conifer-analysis

Post-process conifer output for downstream statistical analysis.

a unified framework for analysing organisational principles in living organisms

pyorganism

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

FROG

HTML

nf-join-map

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

Nextflow

nf-file-utils

Query files for their type and compression state.

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

travis-release-notes

Semi-automated plasmid sequence verification.

help.github.com

GitHub help guides

JavaScript

plasmid-verification

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

kraken2-bracken-test-db

Nextflow

visual-merge

Visualize package hierarchies and allow for links between different hierarchies.

Transform MetaNetX components information and load them into SQL storage.

metanetx-assets

A python wrapper class for the mfinder C tool.

MfinderWrapper

python-conda-travis

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

Shell

wikidata-analysis

Simple query to table conversion and language analysis.

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

meetup-ipyparallel