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Dan Leehr dleehr

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dleehr / dryad-code-review-checklist.md
Created August 27, 2014 16:00
Checklist for Dryad Code Review

Code Review Checklist

  • Read through the code to ensure it is:
    • Legible
    • Well-commented
    • Free of any "code smells"
  • Ensure the associated documentation is up to date.
  • Compile it on your local machine and test the new functionality.
  • Verify that the change is accompanied by adequate testing code. Verify that the code passes the tests.
@dleehr
dleehr / script.js
Created January 30, 2015 15:29
alert('This is on gist.github.com');
@dleehr
dleehr / copy.cwl
Created July 21, 2015 16:37
CWL Boot2Docker permissions
#!/usr/bin/env cwl-runner
class: CommandLineTool
requirements:
- class: DockerRequirement
dockerImageId: 'ubuntu:latest'
inputs:
- id: "#source"
@dleehr
dleehr / merge-secondary-files.cwl
Created December 8, 2016 20:47
#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: ExpressionTool
requirements:
- class: InlineJavascriptRequirement
inputs:
primary:
type: File
@dleehr
dleehr / keybase.md
Created March 9, 2017 02:22

Keybase proof

I hereby claim:

  • I am dleehr on github.
  • I am leehro (https://keybase.io/leehro) on keybase.
  • I have a public key whose fingerprint is 1CEC 11F4 F29E 68FC 12A4 B067 8A8B 8EAB EEA0 5DB7

To claim this, I am signing this object:

@dleehr
dleehr / lookup_curl.sh
Created November 17, 2017 18:41
crossref CN lookups
#!/bin/bash
curl -SLH "Accept: text/bibliography; style=apa" http://dx.doi.org/$1
@dleehr
dleehr / get_project_size.py
Last active December 1, 2017 15:05
#!/usr/bin/env python
"""
Displays the file size of a DDS Project by ID
Loads config/credentials from ~/.ddsclient
Usage: python3 get_project_size.py c8f46e4d-635a-441a-b309-375818f1f7c1
"""
import sys
from ddsc.config import create_config
from ddsc.core.remotestore import RemoteStore
@dleehr
dleehr / build_workflow.py
Last active June 29, 2018 22:10
from cwlgen.import_cwl import parse_cwl
from cwlgen import File, Workflow
from cwlgen.workflow import InputParameter
# Files in https://github.com/Duke-GCB/bespin-cwl/tree/qiime2-workflow
mkdir_tool = parse_cwl('EMPSingleEndSequences-directory.cwl')
import_tool = parse_cwl('tools-import.cwl')
w = Workflow()
@dleehr
dleehr / exomeseq-preprocessing.cwl
Last active October 5, 2018 13:34
{
"$graph": [
{
"class": "Workflow",
"inputs": [
{
"type": [
"null",
{
"type": "array",
@dleehr
dleehr / exomeseq-gatk4-preprocessing.cwl
Last active November 21, 2018 14:50
Updates with fixes for intervals and after meeting with GAAB
{
"$graph": [
{
"class": "Workflow",
"inputs": [
{
"type": [
"null",
{
"type": "array",