These are chat archives for nextflow-io/nextflow

3rd
Feb 2018
Vladimir Kiselev
@wikiselev
Feb 03 2018 19:05
Is the bin folder inside the pipeline directory automatically added to the PATH? Whe I run my pipeline by calling the files in the bin folder, NF does not see them and complains that they don’t exist.
Alexander Peltzer
@apeltzer
Feb 03 2018 19:11
Weird, I thought it does that automatically, see here: https://www.nextflow.io/docs/latest/faq.html#how-do-i-invoke-custom-scripts-and-tools
Vladimir Kiselev
@wikiselev
Feb 03 2018 20:03
thanks, Alexander! Can activation of conda environment change this behaviour? This is what I do before running NF.
Vladimir Kiselev
@wikiselev
Feb 03 2018 20:12
ok, looks like I figured it. I run a local copy of the pipeline. The error occured when I ran it with tilda nextflow run ~/RNAseq. When I changed it to $HOME it worked well: nextflow run $HOME/RNAseq.