These are chat archives for nextflow-io/nextflow

18th
Feb 2019
Paolo Di Tommaso
@pditommaso
Feb 18 07:44
It makes sense, open an issue or draft a PR on GitHub and will continue the discussion there.
David Mas-Ponte
@davidmasp
Feb 18 15:09
Hello, I may have asked this in the past but I fell into the same problem again, sorry for that. So I see that in the .command.run script, the conda environtment is activated using source activate 'path/to/envir'. Is there a reason why nextflow is using source activate instead of conda activate? Apparently conda activate is the prefered way to activate an environtment (see this as reference )
For context, I am trying to use local environtments
*conda local environtments (like here)
Jonathan Manning
@pinin4fjords
Feb 18 16:41
Hi- can I supply lists via the Nextflow config? If not, what's the simplest workaround- e.g. to convert a comma-separated string to numeric list? (sorry, my Groovy Googling is failing me)
lastwon1216
@lastwon1216
Feb 18 16:49
@pditommaso what do you mean by file_var.baseName? is it different from what I did? i set reads=*.fastq.gz and ${reads.baseName}, but was getting something I expected..
lastwon1216
@lastwon1216
Feb 18 17:11
it doesn't only get the part 'test' from test.fastq.gz, but 'test.fastq'
Laurence E. Bernstein
@lebernstein
Feb 18 18:22
I'm not sure how one is supposed to use .baseName or .simpleName. I have a input parameter:
params.reference = "/seq/Resources/hg19-chr7m-22m.fasta"
but I can't use baseName or simpleName with
referenceBase = paramas.reference.baseName or
referenceBase = ${paramas.reference.baseName} or any other variation I've tried.
Paolo Di Tommaso
@pditommaso
Feb 18 19:04
@pinin4fjords list are defined as foo = [1,2,'str', false, ... ]
@lebernstein .baseName / .simpleName are file attributes therefore
referenceBase = file(paramas.reference).baseName
or in file handles in a process execution context
@lastwon1216 broken thread, make an example
KochTobi
@KochTobi
Feb 18 19:10
@pditommaso is there a way to tell nextflow where to put the .nextflow.log file or is it always in the folder the workflow was executed from?
Paolo Di Tommaso
@pditommaso
Feb 18 19:23
nextflow -log <file/path> run .. etc
anybody in san diego/bay area interested to present containerised workflow are Singularity meetup ?
KochTobi
@KochTobi
Feb 18 19:26
@pditommaso Thanks!!
tbugfinder
@tbugfinder
Feb 18 19:36
Hi, I'd like to run singularity within SGE executor. Singularity is installed to /opt/singularity/bin. How could the singularity installation path has to be added to the SGE environment?
Paolo Di Tommaso
@pditommaso
Feb 18 19:42
no experience with that
but I think it's a matter for environment config, independently sge
(make sure you are using bash as shell)
tbugfinder
@tbugfinder
Feb 18 20:09
Hm, .command.run includes / executes PATH="$PATH" SINGULARITYENV_TMP="$TMP" SINGULARITYENV_TMPDIR="$TMPDIR" singularity exec. I tried using env.PATH to extend it but failed so far.
lastwon1216
@lastwon1216
Feb 18 20:11

@pditommaso

params.reads="$PWD/*.fastq.gz"

i tried this too, but comes out as "test.fastq":

readsBase=file(params.reads).baseName
tbugfinder
@tbugfinder
Feb 18 20:16
looks like process.clusterOptions = '-v $PATH:/opt/singularity/bin -V'passes it properly.