Phil Ewels ewels

## 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")

## NF_logo.png
Save NextFlow logo as this file.

## 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.

## 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_*

## 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" />

## 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

## 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             #

## 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();


## .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   ;;

## 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) {