Julian Zaugg julianzaugg

Senior Bioinformatician / Software developer

julianzaugg / nextflow_cleanup_extraneous_work.sh

Created October 15, 2024 10:41 — forked from photocyte/nextflow_cleanup_extraneous_work.sh

	#! /bin/bash

	## See also https://github.com/nextflow-io/nextflow/discussions/4308

	## cd to a parent directory for a Nextflow pipeline executation, i.e. contains .nextflow and work directories

	## Find work directories essential to the last pipeline run, as absolute paths
	nextflow log last > /tmp/preserve_dirs.txt

	## Find all work directories, as absolute paths

julianzaugg / mmseqs_database_GTDB_SSU_reps

Created May 2, 2024 02:08

How to Create database for MMSeqs2 using GTDB SSU reps

	#!/usr/bin/env bash

	# Example of how to create a custom taxonomy database for mmseqs2, e.g. using GTDB SSU sequences from representative genomes

	module load miniconda3/1.1

	BASE=my/data/dir/GTDB_rep_SSUs
	DATABASE_DIR=my/data/dir/GTDB_rep_SSUs/r220_rep_SSU_database

	mkdir -p $DATABASE_DIR

julianzaugg / combine_tsv.R

Last active March 8, 2019 02:10

	# Combine all tsv files in a directory into a single excel spreadsheet

	library(openxlsx)


	file.path2 = function(..., fsep = .Platform$file.sep){

	out <- gsub("//", "/", file.path(..., fsep = fsep))
	}