These are chat archives for nextflow-io/nextflow

28th
Jul 2016
Sandeep Shantharam
@machbio
Jul 28 2016 01:07
@pditommaso - I overcomplicated the workflow; here is what I ended up with - thanks for the groovy help - I am still learning - "nextflow main.nf --in sample.json" solves this
sequences = file(params.in)
new groovy.json.JsonSlurper().parseText(sequences.text).each { k, v -> params[k] = v }

println params.alpha
println params.beta
As I said, I am still learning - does groovy "sequences.text" support us to specify encoding information - like "sequences.text.getText('UTF-8')"
UTF-8 works out of the box - I checked.
Paolo Di Tommaso
@pditommaso
Jul 28 2016 08:04
@jbyars no, output to stderr is not considered an error condition (there are a lot of tools that use it for logging, etc)
@machbio that's an option, however I'm starting to think that a command line option to import a json parameter file could have sense
Sandeep Shantharam
@machbio
Jul 28 2016 13:50
@pditommaso Yes, that would be a better way than confining to only parameters through command line - upstream to the nextflow - we can have a json validator or even validator inside the nextflow process itself - before starting processing - as json and yaml standards.. I will be happy to contribute, if you let me know what would be the best way to proceed from here..
Paolo Di Tommaso
@pditommaso
Jul 28 2016 14:24
That would be nice, you may want to open an issue on the GH repo and continue the discussion there
tx
Stephen Turner
@stephenturner
Jul 28 2016 20:11
just starting to tinker around with nextflow after getting fed up with make. trivial question - what syntax highlighter do you recommend for a text editor? You don't happen to have a sublime text bundle do you?
Paolo Di Tommaso
@pditommaso
Jul 28 2016 20:12
nextflow is a DSL built as a super set of the groovy lang
though not complete you can use any editor having a support for groovy
BTW nextflow pipelines are very concise, personally I never felt the lack of a syntax highlighter