These are chat archives for nextflow-io/nextflow

11th
Mar 2019
Guillaume Theaud
@GuillaumeTh
Mar 11 01:03
Hi, When I launch a pipeline on a SLURM cluster, the .out is pretty hard to read due to multiple duplicate of the output (since the new display). Do you have any tips to solve this ? The old display is yet available ?
Rad Suchecki
@rsuchecki
Mar 11 02:08
-ansi-log false
Paolo Di Tommaso
@pditommaso
Mar 11 08:17
or export NXF_ANSI_LOG=false
Guillaume Theaud
@GuillaumeTh
Mar 11 11:08
Ok thank you very much !
Matthew Pocock
@drdozer
Mar 11 13:47
@pditommaso thanks! I'll see if the boss is up for me attending. Is there a call for papers or presentations open?
Paolo Di Tommaso
@pditommaso
Mar 11 13:48
we'll a call for presentation and tutorials soon, not papers tho
Matthew Pocock
@drdozer
Mar 11 13:49
cheers - I'm googling for it but not finding hits to the 2019 event - can you link me please?
Paolo Di Tommaso
@pditommaso
Mar 11 13:50
we are working on that these days, in a couple of week we'll announce it
there's still time to Sept .. :joy:
Matthew Pocock
@drdozer
Mar 11 13:51
Great :)
KochTobi
@KochTobi
Mar 11 14:36

I have a question regarding the conda functionality. When using process.conda = 'environment.yml'nextflow starts 2 processes:

conda-env creat --prefix work/conda/envname --file /pwd/environment.yml
conda env creat --prefix work/conda/envname --file /pwd/environment.yml

I use a freshly installed miniconda3. I waited for an extremly long time for the environment to get built (aborted after some hours). When I use the second command before starting to build it manually the workflow the environment is built and nextflow can access it.
Any idea why there are two separate commands run when I start the workflow? Is this normal?

Alexander Peltzer
@apeltzer
Mar 11 14:39
That should help with the solving part at least
Laurence E. Bernstein
@lebernstein
Mar 11 23:01

I am using some python script and I have a value "X"

  script:
  {
  """
    #!/usr/bin/python
    // do some python stuff
    x = "something"
  """
  }

I would like this value (X) to be available to my next process. How can I do this?

Rad Suchecki
@rsuchecki
Mar 11 23:13
if you can output the value as stdout than you could use https://www.nextflow.io/docs/latest/process.html#output-stdout-special-file
Laurence E. Bernstein
@lebernstein
Mar 11 23:46

The way I'm doing it now is to write the value to a file, but then my issue is reading it back in as a single value. I've tried:

  input:
    val projectName from project_name_ch.splitText()

But this has the side effect of adding a "\n" onto the string. If I could get rid of the newline all would be well (although a bit "clunky" imo).

Rad Suchecki
@rsuchecki
Mar 11 23:53
Would this work?
input:
    val projectName from project_name_ch.splitText() { it.trim() }
alternatively you could apply .trim() further down when you use projectName, so projectName.trim()