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) {
	#!/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")
	<!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.
	#!/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_*

	<!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" />
	#' ---
	#' 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
	#!/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 #
	<?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();
	# 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 ;;
	<?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) {