Blog:A list of technical advantages of Snakemake over Nextflow | Cloud solution for Snakemake
3
2
Entering edit mode
14 days ago
Kenny ▴ 30

To summarize:

  • Python is the lingua franca of bioinformatics
  • Nextflow's DSL is overbearing and inconsistently uses Groovy
  • Nextflow channels / tuples lack static type checking and prevent code reuse
  • Snakemake is easier to debug (line number + Python exceptions)
  • Nested configuration in Nextflow causes problems
  • Outputs in Snakemake are more organized

https://blog.latch.bio/p/native-snakemake-support-on-latchbio

Snakemake • 2.1k views
ADD COMMENT
14
Entering edit mode

Not sure what prompted this, but

enter image description here

ADD REPLY
9
Entering edit mode

Python is the lingua franca of bioinformatics

Pretty arguable.

ADD REPLY
1
Entering edit mode

Certainly subjective, but would say that Python is more ubiqutious, as its frequently taught as a beginner language, easier to program in (more expressive + easier to debug) and underlies far more core scientific libraries than Groovy.

What's interesting, if you dig into the nextflow source, is that the choice of Groovy seems to be predicated on the authors stumbling upon an existing dataflow framework rather than choosing the best language for the job and writing one from scratch (http://www.gpars.org/webapp/quickstart/index.html). See eg: https://github.com/nextflow-io/nextflow/blob/master/modules/nextflow/src/main/groovy/nextflow/dag/DAG.groovy.

ADD REPLY
0
Entering edit mode

What you mean: Python is better than Groovy in certain aspects

What you're saying: Python is the goddamn best language in the field

Your response should not have been "certainly subjective" but "I should have added my context of comparison, let me fix it now".

ADD REPLY
7
Entering edit mode

and what is the best text editor : vim or emacs ?

ADD REPLY
2
Entering edit mode

The best text editor is vim (neovim is also acceptable).

ADD REPLY
6
Entering edit mode

The moment one misses that big fat SO downvote botton...

Poor post, not differentiated at all, no elaborate pro/con comparison, just a one-sided and provocative / inflammatory rant to promote your product. Thumbs down.

ADD REPLY
4
Entering edit mode

and what is the best structured format ? yaml, json or xml ?

ADD REPLY
4
Entering edit mode

and what is the best indentation style : tabulations or spaces ?

ADD REPLY
4
Entering edit mode

and what is the best way to farm for thumbs up? three flame posts? or responding to three flame posts?

ADD REPLY
2
Entering edit mode

Dear Kenny, I also experienced the learning curve of Nextflow to be quite steep. However, I would say this post is a rather lacking attempt to place your company blog post, and this is reflected in the pointed responses it has received. Also, I would expect a more balanced approach to the pros and cons. I understand that some design decisions had to be made for your product, but I assume it would dipict more competence to carefully weigh the merits of each WF system against each other and then point out the rationale for your decision.

ADD REPLY
6
Entering edit mode
13 days ago

Personally, I prefer writing a new workflow DSL + engine for each project. If I'm working a language with a particularly strong type system I try to embed them entirely in the type system.

ADD COMMENT
6
Entering edit mode
13 days ago

This is pure clickbait. Very disappointing, and almost just advertising for latchbio (again).

ADD COMMENT
2
Entering edit mode

I understand that this post is meant to promote a bioinformatics startup. I honestly do wish any startup in the field all the best (though most are likely to vanish in a short period of time); it is hard enough to make a profitable business model in this field. I am just wondering if that post is possibly rather detrimental being so one-sided. Also, I am not aware of us having a policy against such posts so far.

ADD REPLY
1
Entering edit mode

If there was a "no shameless promotion" policy, the mods would have removed it.

And anyway it's more effective to leave it up for community ridicule.

ADD REPLY
2
Entering edit mode
10 days ago
Juke34 8.2k

The general mood seems quite negative on that post.
I'm a pro Nextflow person, but what's said in the summarize is mostly true. Maybe trivial but might be useful for a beginner that has to choose between learning Snakemake and Nextflow.
Companies has to find ways to exists, so I guess this post is an acceptable way to do it.
And it is not as one-sided as it looks, there is even a pro-Nextflo paragraph: What Nextflow is good at

This is my point of view, making concessions.

ADD COMMENT
2
Entering edit mode

Good comment. There you see how inflammatory posts even gross people off. I was so annoyed by this post here that in fact did not read the linked content.

ADD REPLY
1
Entering edit mode

Everyone is entitled to their opinions, even strong ones. I think the key is not to present (strong) opinions as facts, and to leave some room for debate by presenting both sides.

ADD REPLY

Login before adding your answer.

Traffic: 1796 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6