peterk87’s gists

peterk87 / nf-villumina.sh

Last active May 23, 2024 21:25

CFIA-NCFAD/nf-villumina Bash wrapper script

	#!/bin/bash

	# Function to handle Ctrl+C
	handle_interrupt() {
	echo -e "\n\033[1;31mERROR:\033[1m Script interrupted by user (Ctrl+C)\033[0m"
	exit 1
	}

	# Set up the trap to catch SIGINT (Ctrl+C)
	trap handle_interrupt SIGINT

peterk87 / .tmux.conf

Created May 10, 2024 19:28

.tmux.conf with QoL improvements and won't give you carpal tunnel

	#######################################################################
	# tmux.conf #
	#######################################################################

	#######################################################################
	# Setting the prefix from C-b to C-a #
	#######################################################################
	set -g prefix C-a

	#######################################################################

peterk87 / multi_container_mulled_hash.py

Last active May 30, 2022 18:30

Get "mulled-v2-{hash}" for multi-package containers (https://github.com/BioContainers/multi-package-containers) comma-delimited multi-package definitions (like in the hash.tsv file)

	#!/usr/bin/env python

	import argparse
	import hashlib
	import sys
	from collections import namedtuple
	from typing import List, Dict, Tuple, Union

	# from https://github.com/galaxyproject/galaxy/blob/f12ee5ce6d602cd4c8b4cfc2112988b84a4f255e/lib/galaxy/tool_util/deps/mulled/util.py#L185
	Target = namedtuple("Target", ["package_name", "version", "build", "package"])

peterk87 / viralrecon-2.3-mosdepth-bed-gz.config

Created February 9, 2022 18:26

nf-core/viralrecon v2.3 Mosdepth config to publish/output BED.GZ files

	// nf-core/viralrecon v2.3
	// specify output of bed.gz files produced by Mosdepth
	process {
	withName: 'MOSDEPTH_GENOME' {
	ext.args = '--fast-mode'
	publishDir = [
	path: { "${params.outdir}/variants/bowtie2/mosdepth/genome" },
	mode: 'copy',
	pattern: "*.{summary.txt,bed.gz}"
	]

peterk87 / MN908947.3-orf1a-orf1b-gene-split.gff

Created February 1, 2022 16:53

SARS-CoV-2 MN908947.3 modified GFF with ORF1ab split into ORF1a and ORF1b for proper SnpEff variant effect analysis of ORF1b

	##gff-version 3
	#!gff-spec-version 1.21
	#!processor NCBI annotwriter
	#!genome-build ASM985889v3
	#!genome-build-accession NCBI_Assembly:GCA_009858895.3
	##sequence-region MN908947.3 1 29903
	##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=2697049
	MN908947.3 Genbank region 1 29903 . + . ID=MN908947.3:1..29903;Dbxref=taxon:2697049;collection-date=Dec-2019;country=China;gbkey=Src;genome=genomic;isolate=Wuhan-Hu-1;mol_type=genomic RNA;nat-host=Homo sapiens;old-name=Wuhan seafood market pneumonia virus
	MN908947.3 Genbank five_prime_UTR 1 265 . + . ID=id-MN908947.3:1..265;gbkey=5'UTR
	MN908947.3 Genbank gene 266 13468 . + . ID=gene-ORF1a;Name=ORF1a;gbkey=Gene;gene=ORF1a;gene_biotype=protein_coding

peterk87 / pangolin.config

Last active February 8, 2022 18:59

Nextflow DSL-2 config for the latest version of Pangolin

	process {
	withName: PANGOLIN {
	container = 'quay.io/biocontainers/pangolin:3.1.20--pyhdfd78af_0'
	}
	}

peterk87 / py-illumina-bam-subsampled-genome-coverage.ipynb

Created August 30, 2021 15:44

This Jupyter Notebook is for generating line plots of genome coverage for reads subsampled from input BAM files for different samples, i.e. what is the genome coverage at a particular depth if you were to randomly subsample 1 to X reads for a particular sample.

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peterk87 / rorate_contig.py

Created June 1, 2021 22:14

Rotate a circular contig to start at the same position as a reference sequence

	#!/usr/bin/env python3
	# coding: utf-8

	import logging
	import subprocess
	from io import StringIO
	from pathlib import Path
	from typing import Optional
	import sys

peterk87 / viralrecon2-modules.config

Last active February 9, 2022 18:24

Custom Mosdepth modules config for nf-core/viralrecon v2.2 to output `.bed.gz` files. Will not work for v2.3

	params {
	modules {
	'illumina_mosdepth_genome' {
	args = '--fast-mode'
	publish_files = ['summary.txt':'', 'per-base.bed.gz':'', 'regions.bed.gz':'']
	publish_dir = 'variants/bowtie2/mosdepth/genome'
	}
	'illumina_mosdepth_amplicon' {
	args = '--fast-mode --use-median --thresholds 0,1,10,50,100,500'
	publish_files = ['summary.txt':'', 'per-base.bed.gz':'', 'regions.bed.gz':'']

peterk87 / simple_covplot.py

Created May 17, 2021 22:37

Create coverage plots for multiple genomes from "samtools depth" tabular outputs

	#!/usr/bin/env python

	from pathlib import Path
	import logging

	import typer
	import numpy as np
	import pandas as pd
	import seaborn as sns
	import matplotlib.gridspec as gridspec

Peter Kruczkiewicz peterk87