A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019
Hi, I'm getting the following error trying to run the (--illumina profile) pipeline on an Azure VM instance, running Ubuntu 18.04:
N E X T F L O W ~ version 19.10.0
Launching `connor-lab/ncov2019-artic-nf` [soggy_gilbert] - revision: c4c617be46 [master]
NOTE: Your local project version looks outdated - a different revision is available in the remote repository [48816ee6e6]
Script compilation error
- file : /home/adminMicroNGS01/.nextflow/assets/connor-lab/ncov2019-artic-nf/main.nf
- cause: Not a valid include definition -- it must specify the module path as a string @ line 7, column 1.
include {articNcovNanopore} from './workflows/articNcovNanopore.nf'
^
Script compilation error
- file : /home/adminMicroNGS01/.nextflow/assets/connor-lab/ncov2019-artic-nf/main.nf
- cause: Not a valid include definition -- it must specify the module path as a string @ line 8, column 1.
include {ncovIllumina} from './workflows/illuminaNcov.nf'
^
Script compilation error
- file : /home/adminMicroNGS01/.nextflow/assets/connor-lab/ncov2019-artic-nf/main.nf
- cause: Not a valid include definition -- it must specify the module path as a string @ line 9, column 1.
include {ncovIlluminaCram} from './workflows/illuminaNcov.nf'
^
3 errors
Hi, I'm getting the following error trying to run the (--illumina profile) pipeline on an Azure VM instance, running Ubuntu 18.04:
Same thing if I clone and specify local repo.
Any suggestions to troubleshoot this?
Thanks! D