Christina Chatzipantsiou cgpu

cgpu / get_content.groovy

Created April 19, 2020 14:36 — forked from kdabir/get_content.groovy

get content from url and write to a file in groovy

	// saving from url to a file (append)
	new File("output.xml") << new URL ("http://some.url/some/path.xml").getText()

cgpu / read-multiple-csv-files.R

Created April 29, 2020 22:31 — forked from apreshill/read-multiple-csv-files

Read multiple csv files into R

	# stack overflow answer from Joran Ellis:
	# http://stackoverflow.com/questions/5319839/read-multiple-csv-files-into-separate-data-frames

	# If the path is different than your working directory
	# you'll need to set full.names = TRUE to get the full
	# paths.
	my_files <- list.files("path/to/files")

	# Further arguments to read.csv can be passed in ...
	all_csv <- lapply(my_files,read.csv,...)

cgpu / sra-paired.sh

Created May 1, 2020 22:59 — forked from slowkow/sra-paired.sh

Check if an SRA file contains paired-end data.

	#!/usr/bin/env bash
	# sra-paired.sh
	# Kamil Slowikowski
	# April 23, 2014
	#
	# Check if an SRA file contains paired-end sequencing data.
	#
	# See documentation for the SRA Toolkit:
	# http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc&f=fastq-dump

cgpu / packer-nextflow.yaml

Created March 17, 2021 20:50 — forked from alanbchristie/packer-nextflow.yaml

An example of a Nextflow Packer file in YAML

	---

	# Packer machine image configuration for a Nextflow/Docker machine.
	#
	# To use this file (Packer expects a JSON file) you need to
	# use the project's yaml2json module to convert it to JSON.
	# From this directory and a Suitable Python (see root's requirements.txt)
	# you can run...
	#
	# ../../../yaml2json.py < nextflow.yml > nextflow.json

cgpu / finddups.nf

Created June 16, 2021 02:05 — forked from lindenb/finddups.nf

workflow nextflow finding duplicated files and creating a bash script to replace the duplicate with a symbolic link