Paolo Di Tommaso pditommaso

💭

Vita brevis, ars longa

CTO & Co-founder of Seqera Labs. Distributed, parallel and reactive programming. Creator of http://nextflow.io.

pditommaso / setupGithubRepo

Created October 26, 2021 15:19 — forked from stephenhardy/setupGithubRepo

Initial setup steps for a git and github project

	-- Initial setup

	mkdir <YOURPROJECT>
	cd <YOURPROJECT>
	git init

	-- Link to GitHub hosted repos

	git remote add origin <[email protected]:YOURACCOUNT/YOURREPO.git>
	git pull origin master

pditommaso / ignite_batch.sh

Created May 2, 2019 17:36 — forked from dtrudg/ignite_batch.sh

Nucleus nextflow ignite sbatch script

	#!/bin/bash
	#SBATCH --job-name=ignite-nf-wordcount
	#SBATCH --output=nf_ignite_%j.log

	# Create the ignite allocation across 4 32GB nodes
	#SBATCH --partition=32GB
	#SBATCH -N 4

	# This creates a random cluster seed, so the ignite cluster can communicate
	# with itself and not clash with other running ignite clusters on Nucleus.

pditommaso / demo.nf

Last active April 21, 2019 09:32 — forked from egonw/demo.nf

Using Bioclipse in Nextflow.

	#!/usr/bin/env nextflow
	@Grab(group='net.bioclipse.bacting', module='managers-cdk', version='0.0.3')
	import net.bioclipse.managers.CDKManager

	params.str = "./data.tsv"
	params.size = 5000

	process splitWikidata {
	input:
	file str from Channel.fromPath(params.str)

pditommaso / dgm.json

Created January 16, 2019 20:58 — forked from wololock/dgm.json

	[
	{
	"name": "org.codehaus.groovy.runtime.dgm$0",
	"allDeclaredConstructors": true,
	"allPublicConstructors": true,
	"allDeclaredMethods": true,
	"allPublicMethods": true
	},
	{
	"name": "org.codehaus.groovy.runtime.dgm$1",

pditommaso / dgm.groovy

Created January 16, 2019 20:56 — forked from wololock/dgm.groovy

	@Grab(group = "org.reflections", module = "reflections", version = "0.9.11")

	import groovy.json.JsonOutput
	import org.codehaus.groovy.reflection.GeneratedMetaMethod
	import org.reflections.Reflections
	import org.reflections.util.ConfigurationBuilder

	def reflections = new Reflections(new ConfigurationBuilder().build())

	def json = reflections.getSubTypesOf(GeneratedMetaMethod).collect {

pditommaso / 00_cmd.sh

Created January 24, 2018 23:14 — forked from lh3/00_cmd.sh

Scripts and command lines to create universal mask for hs37d5

	#
	# generate 01compositional.bed.gz
	#

	# low-complexity by mDUST
	mdust hs37d5.fa -c -w7 -v28 \
	\| hs37d5.mdust-w7-v28.txt \
	\| cut -f1,3,4 \
	\| gawk -vOFS="\t" '{--$2;print}' \
	\| bgzip > 01compositional/hs37d5.mdust-w7-v28.bed.gz

pditommaso / raid_ephemeral.sh

Last active December 23, 2017 23:14 — forked from joemiller/raid_ephemeral.sh

detect all ephemeral disks on EC2 then stripe together in a raid-0 vol mounted at /mnt

	#!/bin/bash
	#
	# this script will attempt to detect any ephemeral drives on an EC2 node and create a RAID-0 stripe
	# mounted at /mnt. It should be run early on the first boot of the system.
	#
	# Beware, This script is NOT fully idempotent.
	#
	METADATA_URL_BASE="http://169.254.169.254/2012-01-12"

	yum -y -d0 install mdadm curl

pditommaso / NF_logo.png

Created June 14, 2017 15:53 — forked from ewels/NF_logo.png

NextFlow Multipart HTML Emails

Save NextFlow logo as this file.

pditommaso / Hello.g4

Created March 26, 2017 13:55 — forked from mattmcd/Hello.g4

Simple ANTLR4 grammar example

	// define a grammar called Hello
	grammar Hello;
	r : 'hello' ID;
	ID : [a-z]+ ;
	WS : [ \t\r\n]+ -> skip ;

pditommaso / diff2html.sh

Created September 23, 2016 09:49 — forked from stopyoukid/diff2html.sh

Script that takes a git diff and outputs an html file in GitHub style

	#!/bin/bash
	#
	# Convert diff output to colorized HTML.
	# (C) Mitch Frazier, 2008-08-27
	# http://www.linuxjournal.com/content/convert-diff-output-colorized-html
	# Modified by stopyoukid
	#

	html="<html><head><meta charset=\"utf-8\"><title>Pretty Diff</title><style>body {text-align: center;}#wrapper {display: inline-block;margin-top: 1em;min-width: 800px;text-align: left;}h2 {background: #fafafa;background: -moz-linear-gradient(#fafafa, #eaeaea);background: -webkit-linear-gradient(#fafafa, #eaeaea);-ms-filter: \"progid:DXImageTransform.Microsoft.gradient(startColorstr='#fafafa',endColorstr='#eaeaea')\";border: 1px solid #d8d8d8;border-bottom: 0;color: #555;font: 14px sans-serif;overflow: hidden;padding: 10px 6px;text-shadow: 0 1px 0 white;margin: 0;}.file-diff {border: 1px solid #d8d8d8;margin-bottom: 1em;overflow: auto;padding: 0.5em 0;}.file-diff > div {width: 100%:}pre {margin: 0;font-family: \"Bitstream Vera Sans Mono\", Courier, monospace;font-size: 12px;line-height: 1.4em;text-indent: 0.5em;}.file {color: