These are chat archives for nextflow-io/nextflow

6th
Apr 2018
Paolo Di Tommaso
@pditommaso
Apr 06 2018 07:01
@yamad that's specified in the docs, have a look at the note (blue box)
Félix C. Morency
@fmorency
Apr 06 2018 15:54
@pditommaso would it be preferable to add a note in the documentation about the #562 workaround?
Paolo Di Tommaso
@pditommaso
Apr 06 2018 15:54
we accept PRs :)
Félix C. Morency
@fmorency
Apr 06 2018 15:55
:D
Mark Hollenbeck
@merky
Apr 06 2018 17:28

In my config file (in a profile), I'm specifying docker.enabled as follows (safe property):

docker.enabled = "${USE_DOCKER?:''}"!=""

as per specified here: https://www.nextflow.io/docs/latest/config.html#config-variables. However, when USE_DOCKER env var is not present, I'm getting the error ERROR ~ Unknown config attribute: USE_DOCKER. This is not the expected behavior, but then again Groovy and Nextflow are new to me. Any help?

Mark Hollenbeck
@merky
Apr 06 2018 19:40

Hi again! Sorry, another question: I have outputs in proc2 as follows (notice the globs):

output:
file 'channel*.json'   into ts_channels mode flatten
file 'channel*.ts.bin' into ts_channel_data mode flatten

and would like to have inputs into proc2 as set pairs, e.g. [("channel1.json", "channel1.ts.bin"), ("channel2.json", "channel2.ts.bin"), ...]. I accomplished this using the following in proc2:

input:
set file('channel_info.json'), val(ch_data_file) from ts_channels.merge(ts_channel_data)

However, in some circumstances, I was getting "mismatched" pairs, e.g. ("channel1.json", "channel2.ts.bin"). How can I guarantee proper pairing of the ouputs/inputs?

Mark Hollenbeck
@merky
Apr 06 2018 19:46
Okay, I just figured out the latter question! Very silly. We have many outputs (more than 10), and thus need to pad filenames with 0s... channel001.json, etc. :wink:
Mike Smoot
@mes5k
Apr 06 2018 19:47
I don't think there's any guarantee that'll give you the right order. I think you'd need to sort your channels to be sure.
Mark Hollenbeck
@merky
Apr 06 2018 21:05
Ah, okay, thanks!