New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

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

Merged
merged 5 commits into from Jun 9, 2017

Conversation

3 participants
@tiagofilipe12
Member

tiagofilipe12 commented Jun 5, 2017

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 Jun 5, 2017

@codecov-io

This comment has been minimized.

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

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 7405aa2...ab4f92d. Read the comment docs.

@thejmazz

This comment has been minimized.

Member

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

This comment has been minimized.

@thejmazz

thejmazz Jun 8, 2017

Member

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}`

This comment has been minimized.

@thejmazz

thejmazz Jun 8, 2017

Member

might be worthwhile to use

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

before introducing ES6 syntax

This comment has been minimized.

@tiagofilipe12

tiagofilipe12 Jun 8, 2017

Member

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()

This comment has been minimized.

@thejmazz

thejmazz Jun 8, 2017

Member

mention that it returns a promise, and also can take a callback

@thejmazz

This comment has been minimized.

Member

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

This comment has been minimized.

Member

tiagofilipe12 commented Jun 8, 2017

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

This comment has been minimized.

Member

tiagofilipe12 commented Jun 9, 2017

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

4 checks passed

codecov/patch Coverage not affected when comparing 7405aa2...ab4f92d
Details
codecov/project 80.64% remains the same compared to 7405aa2
Details
continuous-integration/travis-ci/pr The Travis CI build passed
Details
security/snyk No new vulnerabilities
Details

@bmpvieira bmpvieira added this to In Progress in Bionode Project Board Jun 13, 2017

@tiagofilipe12 tiagofilipe12 moved this from In Progress to Done in Bionode Project Board Jun 30, 2017

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment