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Adds a new example pipeline and edits existing example pipeline #53

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merged 5 commits into from
Jun 9, 2017

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tiagofilipe12
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This PR adds a new example pipeline intended do document an easy to use tutorial with simple NGS tools. Also it adds some changes to the existing variant calling pipeline by adding changing the size of the download size of reads to a smaller one, reducing the time to download reads as well as the download size itself.

@tiagofilipe12 tiagofilipe12 self-assigned this Jun 5, 2017
@tiagofilipe12 tiagofilipe12 requested a review from thejmazz June 5, 2017 14:38
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codecov-io commented Jun 5, 2017

Codecov Report

Merging #53 into master will not change coverage.
The diff coverage is n/a.

Impacted file tree graph

@@           Coverage Diff           @@
##           master      #53   +/-   ##
=======================================
  Coverage   80.64%   80.64%           
=======================================
  Files          36       36           
  Lines         806      806           
  Branches       99       99           
=======================================
  Hits          650      650           
  Misses        156      156

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@thejmazz
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thejmazz commented Jun 8, 2017

I think the tutorial should use require('bionode-watermill') instead of require('../../../'). It would then need a little bit more instructions before to do something like:

mkdir watermill-tutorial
cd watermill-tutorial
npm init
npm install --save bionode-watermill

or maybe

git clone tutorialRepoOrBranch

const watermill = require('../../..') /* don't forget to edit this require if
you run it outside bionode-watermill examples/pipelines/simple_tutorial
folder */
const task = watermill.task /* have to specify task since bionode-watermill
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task is not an operator

params: 'Test_file.txt', /*defines parameters to be passed to the
task function*/
name: 'This is the task name' //defines the name of the task
}, ({ params }) => `touch ${params}`
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might be worthwhile to use

function (resolvedProps) {
  const params = resolvedProps.params
  // ...
}

before introducing ES6 syntax

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I think you have a point. ES6 is not standard js, so we should exemplify it first with standard js.

Then after defining the task, it may be executed like this:
```javascript
// runs the task
simpleTask()
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mention that it returns a promise, and also can take a callback

@thejmazz
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thejmazz commented Jun 8, 2017

Oh OK i see you have another "how to use in your project" part. Hmm ok, I'm not sure if ../../../ is going to be confusing to people new to node, but its probably not such a big deal.

@tiagofilipe12
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For now, i think the best pratice for the tutorial would be to require('bionode-watermill') instead of the require('../../..'). Therefore, to make it less confusing, for the user, maybe the best way is to create a new repo that the user just have to clone in order to make the tutorial. Because it might be confusing where to create the new directory, since if you make the new diretory inside the bionode-watermill folder it won't work.
So, for this PR I will just leave the new example pipeline and the changes in the previous pipeline, to reduce the download size from NCBI. The rest of the tutorial I will create a new repo with specific instructions on how to do it.

@tiagofilipe12
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I have removed the tutorials and created a new repo for the tutorial. So, here I just left the new pipeline example a minor change to .gitignore and some minor fixes to the variant-calling-filtered.

@thejmazz thejmazz merged commit 78b5e97 into bionode:master Jun 9, 2017
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3 participants