Skip to content

Instantly share code, notes, and snippets.

Phil Ewels ewels

Block or report user

Report or block ewels

Hide content and notifications from this user.

Learn more about blocking users

Contact Support about this user’s behavior.

Learn more about reporting abuse

Report abuse
View GitHub Profile
@ewels
ewels / trace2json.py
Created Sep 14, 2017
Convert Nextflow Trace text file to JSON format
View trace2json.py
#!/usr/bin/env python
# Convert Nextflow text file to JSON format
import json
headers = []
data = {'trace': []}
with open ('NGI-RNAseq_trace.txt') as fh:
for l in fh:
s = l.split("\t")
@ewels
ewels / NF_logo.png
Created Jun 14, 2017
NextFlow Multipart HTML Emails
View NF_logo.png
Save NextFlow logo as this file.
@ewels
ewels / bioconda_badges.html
Created Aug 24, 2016
Bioconda Poster Badges
View bioconda_badges.html
<!DOCTYPE html>
<html lang="en">
<head>
<!--
BIOCONDA POSTER BADGE GENERATOR
Author: Phil Ewels <phil.ewels@scilifelab.se> (@ewels)
Date: August 2016
To add more templates, create in Adobe Illustrator.
@ewels
ewels / check_bismark_analysis.sh
Last active Aug 18, 2016
Quick and dirty script to check for common warning signs in a Bismark BS-seq methylation analysis
View check_bismark_analysis.sh
#!/bin/bash
# Check bisulfite analysis results for any modes of failure that I can think of.
# Assumes data is processed by Cluster Flow / bismark and is in subdirectories.
# For a basic quick summary, just run:
# bash check_bismark_analysis.sh
# To filter which subdirectories are checked, pass a glob expression. For example:
# bash check_bismark_analysis.sh run2_*
View rcolorbrewer_example.html
<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<meta name="generator" content="pandoc" />
@ewels
ewels / sra_illumina_stats.r
Created Sep 18, 2014
SRA Sequencing Platform Statistics
View sra_illumina_stats.r
#' ---
#' title: "SRA Sequencing Platform Analysis"
#' author: "Phil Ewels"
#' date: September 2014
#' ---
#' The Sequence Read Archive [(SRA)](http://www.ncbi.nlm.nih.gov/sra)
#' contains the raw DNA-sequencing data for many published datasets.
#' We were interested in which sequencing platforms were prevalent,
#' or rather, how prevalent Illumina Sequencing is. We were specifically
@ewels
ewels / cytobands.pl
Created Sep 17, 2014
Cytoband Coordinate Converter
View cytobands.pl
#!/usr/bin/perl
use CGI::Carp qw(fatalsToBrowser); # pipe errors to the browser instead of the terminal for debugging
use warnings;
use strict;
use Data::Dumper;
#print Dumper(\%args);
print "Content-type: text/plain\n\n";
#############################################################
# Name: Cytobands - Coordinates: Online Version #
@ewels
ewels / front-page.php
Created Aug 27, 2014
Child front-page.php for a full width carousel using the Unite wordpress theme: https://github.com/puikinsh/Unite-Theme
View front-page.php
<?php
if ( get_option( 'show_on_front' ) == 'posts' ) {
get_template_part( 'index' );
} elseif ( 'page' == get_option( 'show_on_front' ) ) {
get_header();
while ( have_posts() ) : the_post();
@ewels
ewels / .bashrc
Created Aug 27, 2014
Bash function to extract any compressed file. Code snippet stolen from @robinandeer - https://github.com/robinandeer/dotfiles
View .bashrc
# One command to extract them all
extract () {
if [ $# -ne 1 ]
then
echo "Error: No file specified."
return 1
fi
if [ -f $1 ] ; then
case $1 in
*.tar.bz2) tar xvjf $1 ;;
@ewels
ewels / front-page.php
Created Mar 24, 2014
Example theme code for Bootstrap Feature Widgets plugin
View front-page.php
<?php
// Outputting the widget area on your homepage
// Accomodates one to four active widget areas, fits bootstrap columns accordingly
// front-page.php
$widget_count = 0;
for ($i = 1; $i <= 4; $i++){
if ( is_active_sidebar('homepage-widget-area-'.$i) ) $widget_count++;
}
if ( $widget_count > 0) {
You can’t perform that action at this time.