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bashmacosnextflowrna-seq

ERROR when trying to run Nextflow for RNAseq on MacOSX (M2)

The error I am getting is this right when I try to download the pipeline and test it on a minimal dataset with a single command:

$ nextflow run nf-core/rnaseq -profile test,conda --outdir /Users/aggardik/workflow
N E X T F L O W  \~  version 0.30.1
Launching `nf-core/rnaseq` \[jovial_nightingale\] - revision: 6e1e448f53 \[master\]
ERROR \~ Unknown config attribute `params.genomes.GRCh37.projectDir` -- check config file: /Users/aggardik/anaconda3/envs/RNAseq/share/nextflow/assets/nf-core/rnaseq/nextflow.config

\-- Check '.nextflow.log' file for details
(RNAseq)
Solution

  • Two things I think are needed here:

    • A newer version of Nextflow which enables DSL2 be default; and
    • To specify a revision when running the workflow

    For example:

    nextflow run nf-core/rnaseq \
    -profile test,conda \
    -revision 3.10.1 \
    --outdir /Users/aggardik/workflow

    Note that release 3.10.1 requires Nextflow >= 22.10.11

    If you installed nextflow using Conda, you could try using conda update nextflow to update Nextflow to the latest version. Otherwise, please see the installation documentation to get started.