nextflow-io/hack17

Paolo Di Tommaso

@pditommaso

{
  "process": "${task.process}",
  "cpus": "${task.cpus}", 
   etc
}

<html>
<body>
<table> 
<tr> <td>process </td> <td>${task.process} </td> </tr>
... blah blah
</table>
</body>
</html>

Luca Cozzuto

@lucacozzuto

ok so you already have support for json? How we can make it?

Phil Ewels

@ewels

The downside is that people have to run a second command after the pipeline finishes, which is not so ideal

Luca Cozzuto

@lucacozzuto

PS: no html please! :)

Phil Ewels

@ewels

HTML! HTML! :tada:

Paolo Di Tommaso

@pditommaso

you see, this is why we need a custom report .. :)

Luca Cozzuto

@lucacozzuto

I agree with NOT re-running nextflow (if possible)

Paolo Di Tommaso

@pditommaso

@ewels no, I'm not suggesting to use a separate command to do that

Toni Hermoso Pulido

@toniher

http://javabeat.net/creating-json-using-groovy/

Paolo Di Tommaso

@pditommaso

the run should be able to do that

Phil Ewels

@ewels

@pditommaso ok then I'm confused :)

Matthieu Foll

@mfoll

how?

Phil Ewels

@ewels

@pditommaso "no,no, like log not in place of run "

Paolo Di Tommaso

@pditommaso

look here

here

and here

Hugues Fontenelle

@huguesfontenelle

still on terrace 3rd floor?

Matthieu Foll

@mfoll

yes

Hugues Fontenelle

@huguesfontenelle

joining soon

Paolo Di Tommaso

@pditommaso

I think they are serving the coffee in front the conf room

Andreas Wilm

@andreas-wilm

RE typos: Pull request sent

Emilio Palumbo

@emi80

question from the tutorial:

why -resume is not the default??

Andreas Wilm

@andreas-wilm

Yes. Why not implement -force instead

Luca Cozzuto

@lucacozzuto

agree

Andreas Wilm

@andreas-wilm

Sorry, I heard this might start a flame war

Hugues Fontenelle

@huguesfontenelle

I'd say spaces, not tabs.

Phil Ewels

@ewels

vim, not emacs? :trollface:

Rickard Hammarén

@Hammarn

why not both?

Hugues Fontenelle

@huguesfontenelle

btw, where are the working groups? 3rd floor terrace has moved away, right?

Luca Cozzuto

@lucacozzuto

too cold we went back to the room

Phil Ewels

@ewels

oh sorry, yeah it got cold and rainy so we moved back to the 4th floor room

Hugues Fontenelle

@huguesfontenelle

room number?

Rickard Hammarén

@Hammarn

4th floor and to the left

Luca Cozzuto

@lucacozzuto

bioinformatics room (468)

Hugues Fontenelle

@huguesfontenelle

Luca Cozzuto

@lucacozzuto

Hi Paolo, do you have an example of template for the nextflow log command?

Toni Hermoso Pulido

@toniher

Log file https://github.com/nextflow-io/nextflow/blob/master/src/main/groovy/nextflow/cli/CmdLog.groovy

Rickard Hammarén

@Hammarn

Bumping the link to the hackmd if anyone is interested; here

David Mas-Ponte

@davidmasp

:+1:

Jose Espinosa-Carrasco

@JoseEspinosa

👌

Phil Ewels

@ewels

For anyone who likes stickers - I just left some MultiQC stickers on the desk near the door

Help yourself!

(Also CAW - our cancer analysis pipeline)

Oskar Lindsjö

@Ackia

Thanks Phil!

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