Cannot find version for nf-schema plugin

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1

Hello,

I am trying to run nf-core rnaseq pipeline and encounter the following error:

WARN: Nextflow self-contained distribution allows only core plugins -- User config plugins will be ignored: nf-schema@2.3.0
ERROR ~ Cannot find version for nf-schema plugin -- plugin versions MUST be specified in offline mode

I am running the pipeline in offline mode, hence included the following plugin in the config file after downloading it

plugins {
    id 'nf-schema@2.3.0'
}

command used to download

nextflow plugin install nf-schema

Both nextflow binary and plug in directory are available in the offline mode. Here is the script I use to invoke the pipeline:

#!/bin/bash
#SBATCH --job-name=rna_mouse
#SBATCH --account=def-tperkins
#SBATCH --cpus-per-task=1
#SBATCH --time=15:00:00
#SBATCH --mem=30G
#SBATCH -o ../logs/rnaseq.%j.out
#SBATCH -e ../logs/rnaseq.%j.err
#
module load StdEnv/2023
module load java/21.0.1
module load apptainer/1.2.4

export SLURM_ACCOUNT=def-tperkins
export SALLOC_ACCOUNT=$SLURM_ACCOUNT
export SBATCH_ACCOUNT=$SLURM_ACCOUNT

export TMPDIR=/scratch/asmab/tmp
export NXF_OFFLINE='true'
export NXF_PLUGINS_DIR=/home/asmab/.nextflow/plugins
export PATH=$PATH:/home/asmab/.local/bin

nextflow run /scratch/asmab/nf-core/nf-core-rnaseq_3.18.0/3_18_0 \
        --input ../raw_data/file/samplesheet.csv \
        --outdir ../analysis/rnaseq_out \
        -c obcf-graham.cfg \
        --gtf ../resources/gencode.vM36.primary_assembly.basic.annotation.gtf \
        --fasta ../resources/GRCm39.primary_assembly.genome.fa \
        -w /scratch/asmab/work \
        -plugins nf-schema@2.3.0
2

Hi @asmariyaz23,

What version of Nextflow are you using? My guess is that it’s a relatively old one. We made some changes to the self-contained distribution last summer which should make it easier to work offline with plugins.

Hopefully if you use a newer version of Nextflow, this log line will go away:

WARN: Nextflow self-contained distribution allows only core plugins -- User config plugins will be ignored: nf-schema@2.3.0

Phil

3

Hi @ewels Here is the version of Nextflow I am using:

[asmab@gra-login2 src]$ nextflow -version

      N E X T F L O W
      version 24.04.4 build 5917
      created 01-08-2024 07:05 UTC (03:05 EDT)
      cite doi:10.1038/nbt.3820
      http://nextflow.io

I have also attached the Nextflow log.

nextflow.log.5.txt (26.1 KB)

4

Yes, please try with Nextflow 24.10.x instead.