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[REVIEW]: A reproducible Snakemake pipeline to analyse Illumina paired-end data from ChiP-Seq experiments #1465

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whedon opened this issue May 21, 2019 · 47 comments

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commented May 21, 2019

Submitting author: @mgalland (marc galland)
Repository: https://github.com/KoesGroup/Snakemake_ChIPseq_PE
Version: v1.2.0
Editor: @brainstorm
Reviewer: @vladsaveliev
Archive: 10.5281/zenodo.3240026

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/6fcc9acc993e02b90a1b9028429b36c7"><img src="http://joss.theoj.org/papers/6fcc9acc993e02b90a1b9028429b36c7/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/6fcc9acc993e02b90a1b9028429b36c7/status.svg)](http://joss.theoj.org/papers/6fcc9acc993e02b90a1b9028429b36c7)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@vladsaveliev, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

  1. Make sure you're logged in to your GitHub account
  2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @brainstorm know.

Please try and complete your review in the next two weeks

Review checklist for @vladsaveliev

Conflict of interest

Code of Conduct

General checks

  • Repository: Is the source code for this software available at the repository url?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • Version: Does the release version given match the GitHub release (v1.2.0)?
  • Authorship: Has the submitting author (@mgalland) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

  • Installation: Does installation proceed as outlined in the documentation?
  • Functionality: Have the functional claims of the software been confirmed?
  • Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
  • Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
  • Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  • Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
  • Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

  • Authors: Does the paper.md file include a list of authors with their affiliations?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?
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commented May 21, 2019

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @vladsaveliev it looks like you're currently assigned as the reviewer for this paper 🎉.

⭐️ Important ⭐️

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

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commented May 21, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented May 21, 2019

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commented May 21, 2019

Review

Snakemake_ChIPseq_PE is a solid Snakemake workflow, designed very much in Snakemake spirit, and makes use of its main features like conda or signularity-based runs. Self-contained assuming you have conda executable installed. Python code is clean, follows PEP guidelines an thus easy to read.

The tool is well documented, pretty clear instructions how to install and test it. One small suggestion is to remove ~/ in this command so it would work assuming a user cloned the repo and changed into it:

conda env create --name chipseq --file ~/envs/global_env.yaml

Feature-wise, one suggestion is the ability to start from BAM files as well. Often you either have an external pre-aligned BAMs, or want to do the heavy lifting with another software and use the workflow just for reporting.

Tests complete without any issues and the output corresponds to the description.

All good from my side.

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commented May 21, 2019

Vlad, Thanks a ton for this! @mgalland, could you please apply the fixes/suggestions and generate a preliminary DOI via Zenodo?

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commented May 21, 2019

@whedon check references

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commented May 21, 2019

Attempting to check references...
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commented May 21, 2019


OK DOIs

- 10.5281/zenodo.2025836 is OK
- 10.1093/bioinformatics/bts480 is OK
- 10.1093/bioinformatics/bty560 is OK
- 10.1038/nmeth.1923 is OK
- 10.1093/bioinformatics/btp352 is OK
- 10.1038/s41592-018-0046-7 is OK
- 10.1093/nar/gkw257 is OK
- 10.1093/bioinformatics/btu170 is OK
- 10.1186/gb-2008-9-9-r137 is OK
- 10.1016/j.cels.2018.03.014 is OK
- 10.1186/s13059-016-0924-1 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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commented May 21, 2019

@mgalland, before you put it on Zenodo, please make sure that:

  1. The paper figures render well, they seem a bit off.
  2. There's better spacing on the enumerations, paragraphs and overall text structure.

Other than that, LGTM.

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commented May 21, 2019

Have to clarify that I don't think that running from BAMs is a requirement to accept the article. Just a suggestion. Can go as is.

Agree about the figure rendering though, images look cropped by the right edge, especially the DAG plot.

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commented May 21, 2019

Yes, running from BAMs would be nice but, in practice, I don't really know how to implement this...
Do you think the figures are cropped because their size is too big? Jihed will look into that tonight (Amsterdam time!).

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commented May 21, 2019

@mgalland Snakemake is just a Python extension, so you can use if-else statements whenever you want, e.g. like that:
https://github.com/umccr/10x/blob/master/ema/Snakefile#L49-L75
https://github.com/vladsaveliev/vcf_stuff/blob/master/vcf_stuff/eval_vcf/vcf.smk#L137-L156
Hope this is helpful

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commented May 22, 2019

@whedon generate pdf

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commented May 22, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented May 22, 2019

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commented May 22, 2019

@whedon generate pdf

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commented May 22, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented May 22, 2019

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commented May 22, 2019

@brainstorm Figures seem fine now. Could you be more specific regarding the text formatting? Where would you like to see modifications? Thanks.

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commented May 23, 2019

Thanks @mgalland, looks better now. I was referring to the enumeration after "The outputs delivered with the pipeline are:"... an few extra newlines specifically there and better separation of paragraphs could improve readability. It is now a bit too compact imho.

After this is addressed, feel free to deposit on Zenodo. Cheers!

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commented Jun 3, 2019

@whedon generate pdf

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commented Jun 3, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented Jun 3, 2019

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commented Jun 3, 2019

@whedon generate pdf

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commented Jun 3, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented Jun 3, 2019

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commented Jun 4, 2019

@whedon generate pdf

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commented Jun 4, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented Jun 4, 2019

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commented Jun 4, 2019

@brainstorm I'm very sorry but after several tries, it seems that I cannot add any extra lines to the paper.md file somehow. I don't understand why to be honest. Is that something you'd know about?

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commented Jun 6, 2019

@mgalland I see, my point was that spacing were similar to the GH-rendered markdown version https://github.com/KoesGroup/Snakemake_ChIPseq_PE/blob/master/paper.md, but there might be other tricks to display it well on @arfon's JOSS renderer.

Nevermind, looks good anyway, it was just a minor spacing detail. Looks good to me, could you generate a Zenodo DOI so that it can be archived?

Thanks everyone!

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commented Jun 6, 2019

@brainstorm Thanks! Done! I've made a Zenodo record just know. Thanks to all reviewers and contributors. Here is the link: https://zenodo.org/record/3240026

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commented Jun 6, 2019

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commented Jun 6, 2019

https://zenodo.org/record/3240026 doesn't look like an archive DOI.

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commented Jun 6, 2019

@whedon set 10.5281/zenodo.3240026 as archive

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commented Jun 6, 2019

OK. 10.5281/zenodo.3240026 is the archive.

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commented Jun 6, 2019

All camera ready, @arfon ;)

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commented Jun 6, 2019

@whedon accept

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commented Jun 6, 2019

Attempting dry run of processing paper acceptance...
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commented Jun 6, 2019


OK DOIs

- 10.5281/zenodo.2025836 is OK
- 10.1093/bioinformatics/bts480 is OK
- 10.1093/bioinformatics/bty560 is OK
- 10.1038/nmeth.1923 is OK
- 10.1093/bioinformatics/btp352 is OK
- 10.1038/s41592-018-0046-7 is OK
- 10.1093/nar/gkw257 is OK
- 10.1093/bioinformatics/btu170 is OK
- 10.1186/gb-2008-9-9-r137 is OK
- 10.1016/j.cels.2018.03.014 is OK
- 10.1186/s13059-016-0924-1 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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commented Jun 6, 2019

Check final proof 👉 openjournals/joss-papers#735

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#735, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
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commented Jun 6, 2019

@whedon accept deposit=true

@whedon whedon added the accepted label Jun 6, 2019

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commented Jun 6, 2019

Doing it live! Attempting automated processing of paper acceptance...
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commented Jun 6, 2019

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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commented Jun 6, 2019

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 openjournals/joss-papers#736
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01465
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

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commented Jun 6, 2019

@vladsaveliev - many thanks for your review and to @brainstorm for editing this submission

@mgalland - your paper is now accepted into JOSS ⚡️🚀💥

@arfon arfon closed this Jun 6, 2019

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commented Jun 6, 2019

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](http://joss.theoj.org/papers/10.21105/joss.01465/status.svg)](https://doi.org/10.21105/joss.01465)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01465">
  <img src="http://joss.theoj.org/papers/10.21105/joss.01465/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01465/status.svg
   :target: https://doi.org/10.21105/joss.01465

This is how it will look in your documentation:

DOI

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