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
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| SRR1631879 | |
| SRR1631880 | |
| SRR1631881 | |
| SRR1631882 | |
| SRR1631883 | |
| SRR1631884 | |
| SRR1631885 | |
| SRR1631886 | |
| SRR1631887 | |
| SRR1631888 |
onertipaday
/ dragonflye.nf
Last active
July 28, 2021 07:36
quick and dirty assembly with dragonflye
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| #!/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
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| --- | |
| 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.
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| #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.
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| 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") |