Paolo Di Tommaso

Login: pditommaso

Company: Comparative Bioinformatics, CRG

Location: Barcelona, Spain

Bio: Research engineer in bioinformatics. Distributed, parallel and reactive programming. Java and Groovy geek. Having fun with http://nextflow.io

Blog:

Blog:

Member of

2. Notredame Lab

Repositories

2015-biogas-cebitec

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2015-nov-docker

Materials for http://dib-training.readthedocs.org/en/pub/2015-11-09-docker.html

Akka-Essentials

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Amazon-S3-FileSystem-NIO2

An S3 File System Provider for Java 7

antlr-hello

Classic Hello world example for ANTLR4 grammar parser

ast-workshop

Unleashing the power of AST transformations

awesome-c

A curated list of awesome C frameworks, libraries, resources and other shiny things. Inspired by all the other awesome-... projects out there.

awesome-ci

A curated list of awesome continuous integration services

awesome-containers

null

awesome-db

A curated list of awesome DBs

awesome-java

A curated list of awesome Java libraries

awesome-machine-learning

A curated list of awesome Machine Learning frameworks, libraries and software.

awesome-pipeline

A curated list of awesome pipeline toolkits inspired by Awesome Sysadmin

awesome-schedulers

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awesome-shell

A curated list of awesome command-line frameworks, toolkits, guides and gizmos. Inspired by awesome-php.

awesome-sysadmin

A curated list of amazingly awesome open source sysadmin resources inspired by Awesome PHP.

aws-week-in-review

The files in this GitHub Repo are used to produce the AWS Week in Review.

azure-sdk-for-java

Azure Management Libraries for Java

benchtools

I/O benchmark tools

bigdata-ecosystem

BigData Ecosystem Dataset

bioconda-recipes

Conda recipes for the bioconda channel.

BioNextflow

Nextflow functions for biological tools

Black-Coffee

A black box headless test runner environment

bytebuddy-sandbox

A sandbox for ByteBuddy experiments

capsule

Dead-Simple Packaging and Deployment for JVM Apps

capsule-maven

null

CAW

Cancer Analysis Workflow prototype

ccle-benchmark

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chronicle-minimal

null

circo

Clustering system for the cloud

clashofthelambdas

Microbenchmarking collections via the functional APIs of Java 8, Scala, C#, F#.

companion

Pipeline for automatic eukaryotic parasite annotation

concTree

Using Alignment Uncertainty from Many Multiple Sequence Alignments to Create Consensus Trees

condor-kubernetes

HTCondor dockerized for Kubernetes

cookiecutter

Template for your own top-end Nextflow pipeline, customised using Cookiecutter

Creative-Commons-Markdown

Markdown-formatted Creative Commons licenses

CRG

null

d3-timeline

Simple JS timeline plugin for d3

disni

DiSNI: Direct Storage and Networking Interface

distiller-nf

a modular Hi-C mapping pipeline

docker2singularity

A docker image for converting docker images to singularity images.

docker-cheat-sheet

Docker Cheat Sheet

drip

Fast JVM launching without the hassle of persistent JVMs.

drops

null

easyconfigs

Repository for custom EasyBuild easyconfig files

eatmemory

Simple C program to allocate memory from the command line. Useful to test programs or systems under high memory usage conditions

ec2instances.info

Amazon EC2 instance comparison site

embeded-analysis-nf

Analysis to determine the effect of the inclusion of more sequences in large MSA

FA-nf

Functional annotation pipeline for proteins from non-model organisms implemented in Nextflow

fib-benchmark

null

filepizza

:pizza: Peer-to-peer file transfers in your browser

flow

Consensus assembly and variant calling workflow.

fuse-jna

No-nonsense, actually-working Java bindings to FUSE using JNA.

ga4gh-sandbox

null

gatk4-HaplotypeCaller-nf

GATK4 HaplotypeCaller step, in gVCF mode, first step for subsequent whole cohort Joint Genotyping.

gatk-swe

GATK pipeline compatible with Cirrus

gc-count

null

GPars

The GPars concurrency and parallelism framework for the JVM

gradle-nexus-staging-plugin

Gradle Nexus staging plugin

gradle-test

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grape-nf

An automated RNA-seq pipeline using Nextflow

grengine

Grengine is an engine for running and embedding Groovy in a Java VM.

groovy

Mirror of Apache Groovy

groovy_2.3_bug

null

groovy-common-extensions

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groovy-core

Groovy language Git repository

groovycsv

A simple CSV parsing library for groovy

groovy-jet-aot

Groovy sandbox for AOT native compilation

groovy-parser

Create a brand new parser for Groovy programming language(project code: Parrot)

GSoC

OBF Google Summer of Code

gsoc16

GSoC Project: Streaming Workflow Engine

gspark

Sandbox testing Groovy based Spark applications

h3abionet16S

H3ABioNet 16S package

homebrew

The missing package manager for OS X.

homebrew-core

? Default formulae for the missing package manager for macOS

homebrew-science

Scientific formulae for the Homebrew package manager

hts-specs

Specifications of SAM/BAM and related high-throughput sequencing file formats

intellij_bug

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java-string-similarity

Implementation of various string similarity and distance algorithms: Levenshtein, Jaro-winkler, n-Gram, Q-Gram, Jaccard index, Longest Common Subsequence edit distance, cosine similarity ...

jbake

Java based open source static site/blog generator for developers & designers.

jclouds-site

Mirror of Apache jclouds site source repo

jsr203-hadoop

A Java NIO file system provider for HDFS

keybase-gpg-github

Step-by-step guide on how to create a GPG key on keybase.io, adding it to a local GPG setup and use it with Git and GitHub.

kube-primer

Basic Kubernetes primer

kubernetes

Container Cluster Manager from Google

language-groovy

Groovy language support in Atom

libnewicktree

A standalone Newick tree reader in Java

linguist

Language Savant. If your repository's language is being reported incorrectly, send us a pull request!

lncRNA-Annotation-nf

A Nextflow lncRNA Annotation Pipeline based on STAR, Cufflinks and FEELnc

memoryfilesystem

An in memory implementation of a JSR-203 file system

memusg

A 'time'-like utility for Unix that measures peak memory usage

nanoflow

De novo assembly of nanopore reads using nextflow

nextflow-demos

Example Nextflow pipelines and programming techniques

nf-co.re

Files for the main nf-core website >>>

nf-core.github.io

Documentation website for the nf-core community

nf-module-demo

Demo for Nextflow modules and components proposal

nf-syntax-debug

null

nf-toxomix

Nextflow pipeline for toxicology predictions based on transcriptomic profiles

NGI-RNAseq

Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.

NGI-smRNAseq

Nextflow Small RNA Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.

NotesOnJava8

These are my own notes to a week-long Java 8 course.

oneliners

Useful bash one-liners for bioinformatics.

paraMSA

Pipeline for generating multiple sequence alignments and bootstrap replicates

pfff

--

phylo-tutorial-nf

An Introductory Nextflow Tutorial

phyvaluate-nf

Evaluation of Phylogenetic Trees from Simulated Data

picocli

Annotation-based Java command line parser. Usage help with ANSI colors. Easily included as source to avoid adding dependencies.

Pipeline.py

A framework to build pipelines

piper-nf

RNA mapping pipeline

Pi_Quadrature

Various implementations in various languages of approximating ? using quadrature. This is an embarrassingly parallel problem to investigate scaling.

PRoot

chroot, mount --bind, and binfmt_misc without privilege/setup

proteogenomics-analysis-workflow

IPAW: a Nextflow workflow for proteogenomics

protocols

This will be a directory of lab analysis protocols.

raxml-nf

RAxML pipeline

reactive-streams

Reactive Streams Specification for the JVM

repeatable-workflows-docker-ipython

null

rnademo

null

RNAseq-nf

RNAseq analysis pipeline

rnaseq_tutorial

Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.

sandbox

Currently the server isn't running, sorry :)

scalability-reproducibility-chapter

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scalability-reproducibility-chapter-1

Data and workflow examples

shootstrap2

shootstrap + new alternative MSA methods

shuffle-guidance

Nextflow pipeline for creating shuffle and shuffle + Hot/Guidance/Guidance2 alignments

simple-react

Powerful Future Streams & Async Data Structures for Java 8

simple-yarn-app

Simple YARN application

singularity-benchmarks

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singularity-scientific-example

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snv-calling-nf

Nextflow workflow for SNV calling using GATK4 / MuTect2, CaVEMan / Pindel and Strelka2

sparrow

Sparrow scheduling platform (U.C. Berkeley).

spring-flo

JavaScript angular based embeddable graphical component for pipeline/graph building and editing

sra-dump-nf

Some ideas for pulling experiments directly from the SRA with Nextflow

ssl-explorer

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tcs-benchmark

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TensorFlow-for-absolute-beginners

TensorFlow for absolute beginners: a 3-hour codelab for self-learning neural network basics without hard math.

test-lfs

null

the-art-of-command-line

Master the command line, in one page

trace2sing

Trace program execution and create Singularity container for reproducible execution

travis-docker-example

Proof of concept for running docker in a Travis CI build

udocker

A basic user tool to execute simple containers in batch or interactive systems without root privileges

UTC-0500

UTC-500 team submission for the AI Genomics Hackathon, 23-25 June 2017.

vagrant-vbguest

A Vagrant plugin to keep your VirtualBox Guest Additions up to date

vast-tools-nf

A Nextflow Implementation of VAST-TOOLS for profiling alternative splicing events in RNA-Seq data

vipr

nf-core/vipr is a bioinformatics best-practice analysis pipeline for assembly and intrahost / low-frequency variant calling for viral samples

webgl-heatmap

A high performance WebGL/JS heatmap display library

wicket-ext

Automatically exported from code.google.com/p/wicket-ext

YAMP

YAMP: Yet Another Metagenomic Pipeline

Commits To