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connor-lab / ncov2019-artic-nf

A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019
GNU Affero General Public License v3.0
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Access to undefined parameter 'gff' #94

Open hodeco opened 3 years ago

hodeco commented 3 years ago

Hello,

at the very beginning I run into the following problem that I can not find a solution for. Did anybody have the problem before?

Many thanks in advance!

WARN: DSL 2 IS AN EXPERIMENTAL FEATURE UNDER DEVELOPMENT -- SYNTAX MAY CHANGE IN FUTURE RELEASE executor > local (3) [0f/b98f62] process > ncovIllumina:prepareReferenceFiles:articDownloadScheme (https://git... [100%] 1 of 1 ✔ [bc/c2382f] process > ncovIllumina:prepareReferenceFiles:indexReference (nCoV-2019.refere... [100%] 1 of 1 ✔ [- ] process > ncovIllumina:sequenceAnalysis:readTrimming - [- ] process > ncovIllumina:sequenceAnalysis:readMapping - [- ] process > ncovIllumina:sequenceAnalysis:trimPrimerSequences - [- ] process > ncovIllumina:sequenceAnalysis:callVariants - [- ] process > ncovIllumina:sequenceAnalysis:makeConsensus - [- ] process > ncovIllumina:sequenceAnalysis:makeQCCSV - [c1/a1760e] process > ncovIllumina:sequenceAnalysis:writeQCSummaryCSV (210129_test) [100%] 1 of 1 ✔ [- ] process > ncovIllumina:sequenceAnalysis:collateSamples - WARN: Access to undefined parameter gff -- Initialise it to a default value eg. params.gff = some_value

jhill1440 commented 3 years ago

Hello,

I am getting the same issue when running either the docker or singularity profiles.

My command I am running: ./nextflow run connor-lab/ncov2019-artic-nf -profile docker --illumina --prefix test1 --directory /home/

Thanks

dianalir commented 3 years ago

Hello,

I am getting the same issue when running either the docker or singularity profiles.

My command I am running: ./nextflow run connor-lab/ncov2019-artic-nf -profile docker --illumina --prefix test1 --directory /home/

Thanks

@jhill1440 did you manage to solve it?