Closed adamkoletis closed 2 years ago
Sorry about this, we'll push an update to fix. If you want to get it working in the meantime then change the nextflow pangolin process to include a check for internet connectivity like below. If you run without connectivity you won't get the most up to date pangolin, however.
process pangolin {
label "pangolin"
cpus 1
input:
path "consensus.fasta"
output:
path "lineage_report.csv", emit: report
path "pangolin.version", emit: version
"""
# Check to see if the box running the workflow has internet connectivity
echo -e "GET http://nanoporetech.com HTTP/1.0\n\n" | nc nanoporetech.com 80 > /dev/null 2>&1
if [ $? -eq 0 ]; then
pangolin --update
else
echo "Offline"
fi
pangolin --update
pangolin --all-versions 2>&1 | sed 's/: /,/' > pangolin.version
pangolin consensus.fasta
"""
}
sorry - edit to the above - turns out nc is not installed in the docker image for pangolin
process pangolin {
label "pangolin"
cpus 1
input:
path "consensus.fasta"
output:
path "lineage_report.csv", emit: report
path "pangolin.version", emit: version
"""
# Check to see if the box running the workflow has internet connectivity
EXIT_CODE=0
wget -q --spider --timeout 10 http://nanoporetech.com || EXIT_CODE=\$?
if [ \${EXIT_CODE} -eq 0 ]; then
pangolin --update
else
echo "Offline"
fi
pangolin --all-versions 2>&1 | sed 's/: /,/' > pangolin.version
pangolin consensus.fasta
"""
}
@adamkoletis this is fixed as of v0.3.7
Hi Please. I had followed the update but 1)The CHANGELOG.md does not getting any update, I mean showing until v0.3.5 2)Still appears issue with pangolin and internet needs. Thanks
how are you running the workflow?
If you do the following it should pull the latest version
nextflow run epi2me-labs/wf-artic -latest
If you have cloned the repo then you likely need to pull the latest verison:
cd wf-artic
git fetch --tags
git checkout v0.3.7
There is a blog post that explains how to manage our workflows here: https://labs.epi2me.io/managing-epi2me-labs-workflows-with-the-nextflow-command-line-interface/
Please we face the above issue.With no connection internet cannot proceed the pipeline.