These are chat archives for nextflow-io/nextflow
.command.runscript, the conda environtment is activated using
source activate 'path/to/envir'. Is there a reason why nextflow is using
source activateinstead of
conda activate? Apparently
conda activateis the prefered way to activate an environtment (see this as reference )
foo = [1,2,'str', false, ... ]
referenceBase = file(paramas.reference).baseName
filehandles in a process execution context
.nextflow.logfile or is it always in the folder the workflow was executed from?
/opt/singularity/bin. How could the singularity installation path has to be added to the SGE environment?
.command.runincludes / executes
PATH="$PATH" SINGULARITYENV_TMP="$TMP" SINGULARITYENV_TMPDIR="$TMPDIR" singularity exec. I tried using env.PATH to extend it but failed so far.
i tried this too, but comes out as "test.fastq":