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Another day, another workflow DSL. * looks like yaml * has curly braces to look programmery * whitespace might be meaningful * has pipes like a bash sc
by adolph 3y ago
Another day, another workflow DSL.
* looks like yaml
* has curly braces to look programmery
* whitespace might be meaningful
* has pipes like a bash script
https://www.commonwl.org/ https://www.commonwl.org/
https://github.com/common-workflow-language/common-workflow-language/wiki/Existing-Workflow-systems https://github.com/common-workflow-language/common-workflow-...
mea culpa: The above was based on a first look at something titled "A DSL for parallel and and scalable computational pipelines"a as opposed to "Java workflow manager with Groovy language scripting." The presented screenshot still looks to me like an unholy union of yaml, js, py and sh. If that sounds groovy to you; have fun.
- bafe 3y agoIf you refer to nextflow,the syntax is basically groovy
- notQuiteEither 3y agoIndeed, it's a fully functional scripting language that is an extension of groovy. So "looks programmery" is more than a little reductive. Edit: functional as in, it's not half-hearted, not functional as in functional programming.
- adolph 3y agoInteresting. From the docs: The Nextflow scripting language is an extension of the Groovy programming language. Groovy is a powerful programming language for the Java virtual machine. The Nextflow syntax has been specialized to ease the writing of computational pipelines in a declarative manner. https://www.nextflow.io/docs/latest/script.html?highlight=groovy https://www.nextflow.io/docs/latest/script.html?highlight=gr...
- joysofpi 3y agoIts really just a layer on top that uses the groovy DSL features http://docs.groovy-lang.org/docs/latest/html/documentation/core-domain-specific-languages.html http://docs.groovy-lang.org/docs/latest/html/documentation/c...
- esafak 3y agoIn all fairness, they predate the competition (2013): https://github.com/nextflow-io/nextflow/releases?page=25 https://github.com/nextflow-io/nextflow/releases?page=25
- geoffjentry 3y agoAs GP referenced CWL, while NF had appeared first in terms of the bioinformatics world Nextflow, CWL, Snakelike, and WDL all erupted close enough to each other to be equal-ish. The people were aware of each other but they were all so nascent that it wasn't clear if it was worth joining in or not. At the end of the day these all came from groups trying to scratch particular itches, and not everyone agreed on the right way to scratch. However all of them were rejections of prior models as well as the workflow solutions prominent in the business space.
- adolph 3y agoYeah, the thing that I find disappointing is that there is a lot of science value locked into the different systems of describing a workflow, pipeline or DAG. Like you said, they all had different itches to scratch and even some barebones "standards" like csv have flavors/extensions/etc.
- bafe 3y agoThey try to address similar solutions, but comparing snakemake and nextflow doesn't do either tool a favour. They use different computation models, nextflow is based on dataflow programming and therefore schedules processes dynamically as new data comes in, while snakemake is pull-based and schedules the processes based on the dag defined by the dependencies. Anyhow they are both great tools.
- geoffjentry 3y agoWhile true that’s a minor distinction when comparing the clusters of bioinformatics workflow systems vs workflow systems aimed at different domains