Running atacseq/2.1.2/ offline, issue with nf-validation plugin

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1

Hello,

I am trying to run this atacseq pipeline offline (atacseq: Introduction)
It is the first time I am using nextflow and I am using it on a HPC without internet connexion. I have downloaded the .tar.gz for the pipeline and transfered it to the HPC. I am trying to run it with this script :

module load Java/17

export NXF_OFFLINE=‘true’

Répertoire de travail

WORKDIR=/scratch/ulg/immvac/llenoir/benjamin/ATAC-seq_Georgios
cd $WORKDIR

echo “sample,fastq_1,fastq_2” > samplesheet.csv
for R1 in **R1_001.fastq.gz; do
sample=$(echo R1 | cut -d’*’ -f1) R2={R1/R1/R2}
echo “$sample,$R1,$R2” >> samplesheet.csv
done

nextflow run /scratch/ulg/immvac/llenoir/benjamin/ATAC-seq_Georgios/nf-core-atacseq_2.1.2/2_1_2
–input {WORKDIR}/samplesheet.csv –genome GRCm39 –outdir {WORKDIR}/results_atacseq
–read_length 150 \

But I always get this error :

N E X T F L O W ~ version 25.04.6

WARNING: Could not load nf-core/config profiles: https://raw.githubusercontent.com/nf-core/configs/master/nfcore_custom.config
Launching /scratch/ulg/immvac/llenoir/benjamin/ATAC-seq_Georgios/nf-core-atacseq_2.1.2/2_1_2/main.nf [golden_engelbart] DSL2 - revision: cd391b80c9

ERROR ~ Cannot find version for nf-validation plugin – plugin versions MUST be specified in offline mode

– Check script ‘/scratch/ulg/immvac/llenoir/benjamin/ATAC-seq_Georgios/nf-core-atacseq_2.1.2/2_1_2/main.nf’ at line: 39 or see ‘.nextflow.log’ file for more details

Thanks for your help,

Lionel

P.S.: Should I also download the mouse reference genome ? If yes how ?

2

It looks like you don’t have the nf-validation plugin available in your offline environment. You can follow the instructions here to pull the plugin via an online node. Basically:

  1. Download any additional plugins by running nextflow plugin install <pluginId,..>. Alternatively, simply run your pipeline once and Nextflow will download all of the plugins that it needs.

  2. Copy the nextflow binary and $HOME/.nextflow folder to your offline environment.

  3. In your Nextflow configuration file, specify each plugin that you downloaded, both name and version, including default plugins. This will prevent Nextflow from trying to download newer versions of plugins.

If you’re going to use a reference genome, you can find the documentation for downloading the assets here.

3

Thanks for your answer.

I downloaded this plugin nf-validation and have these three plugins :
nf-amazon-2.15.0
nf-schema-2.4.2
nf-validation-1.1.4

Should I modify the nextflow.config file by addind this :

plugins {
id ‘nf-amazon@2.15.0’
id ‘nf-schema@2.4.2’
id ‘nf-validation@1.1.4’
}

in place of this :

plugins {
id ‘nf-validation’ // Validation of pipeline parameters and creation of an input channel from a sample sheet
}

Here is the submission for my offline job if that could be useful :

module load Java/17

export NXF_OFFLINE=‘true’
export NXF_SINGULARITY_CACHEDIR=/scratch/ulg/immvac/llenoir/benjamin/ATAC-seq_Georgios/nf-core-atacseq_2.1.2/singularity-images

WORKDIR=/scratch/ulg/immvac/llenoir/benjamin/ATAC-seq_Georgios
cd $WORKDIR

nextflow run /scratch/ulg/immvac/llenoir/benjamin/ATAC-seq_Georgios/nf-core-atacseq_2.1.2/2_1_2
–input {WORKDIR}/samplesheet.csv –genome GRCm38 –outdir {WORKDIR}/results_atacseq
–read_length 150 \

4

Yes, we encourage workflow authors to pin the plugin versions to make offline use easier. In this case, the nf-core/atacseq authors have not updated to the latest nf-core template, so the plugin remains unpinned. Pinning the plugin version/versions yourself via configuration should be sufficient.