Paolo onertipaday

onertipaday / SRR_Acc_List.txt

Last active January 17, 2022 08:37

nextflow pipeline for aligning RNA-seq samples to Vitis vinifera transcriptome

onertipaday / dragonflye.nf

Last active July 28, 2021 07:36

quick and dirty assembly with dragonflye

	#!/usr/bin/env nextflow

	params.inputDir = "./fastq/*.fastq.gz"
	params.outdir = "./results"

	Channel
	.fromPath(params.inputDir).map { tuple (it.name.split('.fastq.gz')[0], it ) }
	.set { fastq_assemble_ch }

	process dragonflye {

onertipaday / usecase03.Rmd

Last active June 24, 2021 12:12

VESPUCCI Use Case: Genes involved in pollen development

	---
	title: "VESPUCCI Use Case 03"
	author: "Paolo Sonego"
	date: "06/24/2021"
	output: html_document
	---

	```{r setup, include=FALSE}
	knitr::opts_chunk$set(echo = TRUE)
	```

onertipaday / delete_files_timeframe.sh

Created April 13, 2018 07:24

FInding and deleting files bwtween a fixed timeframe.

	#use this to check the files are going to be deleted are the right ones
	find . -maxdepth 1 -type f -newermt '2016-10-12 14:22:59' ! -newermt '2016-10-12 14:24:59'
	# delete them
	find . -maxdepth 1 -type f -newermt '2016-10-12 14:22:59' ! -newermt '2016-10-12 14:24:59' -deleted

onertipaday / download.file2.R

Last active April 11, 2018 12:47

'improved' version of download.file function: you need to specify only the URL of a resource to be downloaded.

	download.file2 <- function (url, destfile = NULL, method, quiet = FALSE, mode = "w", cacheOK = TRUE, extra = getOption("download.file.extra"))
	{
	if (is.null(destfile)) destfile <- basename(url)
	else destfile
	method <- if (missing(method))
	getOption("download.file.method", default = "auto")
	else match.arg(method, c("auto", "internal", "libcurl", "wget",
	"curl", "lynx"))
	if (method == "auto") {
	if (length(url) != 1L \|\| typeof(url) != "character")