Robert A. Petit III rpetit3

	sample	rank	reason	genome_size	species	runtype	original_runtype	mlst_scheme	mlst_st	assembler_total_contig	assembler_total_contig_length	assembler_max_contig_length	assembler_mean_contig_length	assembler_median_contig_length	assembler_min_contig_length	assembler_n50_contig_length	assembler_l50_contig_count	assembler_num_contig_non_acgtn	assembler_contig_percent_a	assembler_contig_percent_c	assembler_contig_percent_g	assembler_contig_percent_t	assembler_contig_percent_n	assembler_contig_non_acgtn	assembler_contigs_greater_1m	assembler_contigs_greater_100k	assembler_contigs_greater_10k	assembler_contigs_greater_1k	assembler_percent_contigs_greater_1m	assembler_percent_contigs_greater_100k	assembler_percent_contigs_greater_10k	assembler_percent_contigs_greater_1k	is_paired	is_compressed	annotator_total_CDS	annotator_total_rRNA	annotator_total_tRNA	qc_original_total_bp	qc_original_coverage	qc_original_read_total	qc_original_read_min	qc_original_read_mean	qc_original_read_std	qc_original_read_median	qc_original_re

	#! /bin/bash
	# A script to submit a SLURM job to run Bactopia Tools on ATB data
	# Expected Options:
	# 1: Bactopia directory
	# 2: Bactopia Tool
	# 3: config file
	# 4: A specific profile to use
	# 5: A specific account to use
	# 6: Where to cache singularity/apptainer images
	BACTOPIADIR=${1}

	#! /bin/bash
	# A script to submit a SLURM job to run bactopia-atb-downloader and bactopia-atb-formatter
	# Expected Options:
	# 1: Organism to download
	# 2: ARCC Account
	# 3: Output Directory
	ORGANISM="${1}"
	LOWERCASE_ORGANISM="${ORGANISM,,}"
	UNDERSCORE_ORGANISM="${LOWERCASE_ORGANISM// /_}"
	ACCOUNT=${2}

	#! /bin/bash

	if [[ $# == 0 ]]; then
	echo ""
	echo "create-user NEW_USERNAME"
	echo ""
	echo "Example Command"
	echo "create-user robert_petit"
	echo ""
	exit

	#! /bin/bash

	if [[ $# == 0 ]]; then
	echo ""
	echo "reset-password NEW_USERNAME"
	echo ""
	echo "Example Command"
	echo "reset-password robert_petit"
	echo ""
	exit

	#! /bin/bash

	if [[ $# == 0 ]]; then
	echo ""
	echo "create-admin NEW_USERNAME"
	echo ""
	echo "Example Command"
	echo "create-admin robert_petit"
	echo ""
	exit

	#!/usr/bin/env python
	"""
	A simple script to query API to get public/private status of all repos under a namespace.

	Caveat being, without an API key, you will only ever see the public repos.
	"""
	PROGRAM = 'quay-namespace-info'
	VERSION = '1.0.0'
	QUAY_API_URL= 'https://quay.io/api/v1/repository'

	/*
	This file includes default values for Teton.
	*/

	process {
	executor = 'slurm'
	queue = 'teton,moran'
	scratch = params.slurm_use_scratch
	time = 60.m
	clusterOptions = '--account healthdatasci'

	#!/usr/bin/env bash

	# ~/.bashrc: executed by bash(1) for non-login shells.

	# If not running interactively, don't do anything
	[ -z "$PS1" ] && return

	# don't put duplicate lines in the history. See bash(1) for more options
	# ... or force ignoredups and ignorespace
	HISTCONTROL=ignoredups:ignorespace