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robsyme / main.nf
Created March 28, 2024 22:47
Publishing oddities
#!/usr/bin/env nextflow
params.outdir = 'results'
params.all = false
workflow {
First()
First.out.value | Second
Second.out.value | Third
@robsyme
robsyme / main.nf
Created March 28, 2024 22:11
Publication behaviour example
#!/usr/bin/env nextflow
params.outdir = 'results'
params.all = false
workflow {
First()
First.out.value | Second
Second.out.value | Third
@robsyme
robsyme / main.nf
Created June 14, 2023 15:54
process A {
input: val(name)
output: tuple val(name), path("*")
script: "echo hello $name > greeting.${name}.txt"
}
process B {
input: val(name)
output: tuple val(name), path("*")
script: "echo goodbye $name > farewell.${name}.txt"
@robsyme
robsyme / main.nf
Created December 9, 2022 20:13
#!/usr/bin/env nextflow
nextflow.enable.dsl=2
nextflow.preview.recursion=true
params.input = 'data/*.dat'
process ScannerLightly {
input:
path datfile_accumulator
val meta_accumulator
@robsyme
robsyme / bar
Created September 9, 2022 21:22
#!/usr/bin/env ruby
require 'json'
require 'optparse'
options = {}
OptionParser.new do |opt|
opt.on('--report FILENAME') { |report| options[:report] = report }
end.parse!
@robsyme
robsyme / main.nf
Last active August 23, 2022 19:57
process A {
input:
val(i)
output:
path("output.${i}.txt")
"echo hello $i > output.${i}.txt"
}
@robsyme
robsyme / Dog.groovy
Created November 26, 2020 21:58
class Dog {
final String name
Dog(String name) {
this.name = name
}
@Override
public int hashCode() {
return name.hashCode()
@robsyme
robsyme / notebook.nb.html
Last active January 23, 2019 00:46
<!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" />
@robsyme
robsyme / Example.sparql
Created April 24, 2012 00:26
Example sparql query for http://i9606.blogspot.fr/2012/04/gene-wiki-sparql-endpoint.html
PREFIX wiki: <http://genewikiplus.org/wiki/Special:URIResolver/>
PREFIX property: <http://genewikiplus.org/wiki/Special:URIResolver/Property-3A>
SELECT ?gene ?disease ?gene_name ?disease_name ?doid
WHERE {
?gene property:Is_associated_with_disease ?disease .
?gene property:HasSNP ?snp .
?snp property:Is_associated_with_disease ?disease .
?gene rdfs:label ?gene_name .
?disease rdfs:label ?disease_name .
?disease rdf:type ?disease_cat .
@robsyme
robsyme / EDAM_topics.tree
Created November 5, 2011 08:00
Bioinformatics topics from EDAM (http://voxel.dl.sourceforge.net/project/edamontology/EDAM_beta12.obo)
* Topic
|---+ Biological data resources
| |---+ Laboratory resources
| |---> Microarrays
| |---> Cell culture resources
| +---> Medical informatics resources
| +---+ Biological science resources
|---> Cell biology resources
|---+ Developmental biology resources
| +---> Embryology resources