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") |
View NF_logo.png
| Save NextFlow logo as this file. |
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
/ 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" /> |
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 |
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
/ 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
/ .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 ;; |
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) { |
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