Conda issues when running the workflow

[guosongjia]

Dear Developers,\ Thanks for your software! I met with the following errors when running the commands using a nextflow environment created under conda env:\ \ (nextflow) [jiaguosong@dulab ~]$ nextflow run hoelzer/pocp -r 2.3.0 --help N E X T F L O W ~ version 0.24.2 Launching hoelzer/pocp [adoring_tesla] - revision: 092166e822 [2.3.0] ERROR ~ Unable to parse config file: '/data/a/jiaguosong/.nextflow/assets/hoelzer/pocp/nextflow.config'

Compile failed for sources FixedSetSources[name='file:/data/a/jiaguosong/.nextflow/assets/hoelzer/pocp/configs/conda.config']. Cause: org.codehaus.groovy.control.MultipleCompilationErrorsException: startup failed: file:/data/a/jiaguosong/.nextflow/assets/hoelzer/pocp/configs/conda.config: 2: you tried to assign a value to the class 'conda'. Do you have a script with this name? @ line 2, column 25. withLabel: prokka { conda = "$baseDir/envs/prokka.yaml" } ^

file:/data/a/jiaguosong/.nextflow/assets/hoelzer/pocp/configs/conda.config: 3: you tried to assign a value to the class 'conda'. Do you have a script with this name? @ line 3, column 24. withLabel: blast { conda = "$baseDir/envs/blast.yaml" } ^

file:/data/a/jiaguosong/.nextflow/assets/hoelzer/pocp/configs/conda.config: 4: you tried to assign a value to the class 'conda'. Do you have a script with this name? @ line 4, column 26. withLabel: diamond { conda = "$baseDir/envs/diamond.yaml" } ^

file:/data/a/jiaguosong/.nextflow/assets/hoelzer/pocp/configs/conda.config: 5: you tried to assign a value to the class 'conda'. Do you have a script with this name? @ line 5, column 23. withLabel: pocp { conda = "$baseDir/envs/diamond.yaml" } ^

file:/data/a/jiaguosong/.nextflow/assets/hoelzer/pocp/configs/conda.config: 6: you tried to assign a value to the class 'conda'. Do you have a script with this name? @ line 6, column 23. withLabel: ruby { conda = "$baseDir/envs/ruby.yaml" } ^

5 errors

-- Check '.nextflow.log' file for details\ \ Could you please give me some advice to solve it?\ Best,\ Guo-Song

[hoelzer]

Hey, thanks for your interest in the tool!

Your nextflow version is very old. Please update nextflow and try again.

You can install nextflow via conda, e.g.

conda create -n nf -c bioconda nextflow
conda activate nextflow

Or following the instructions at the nextflow.io webpage.

You should have at least version >21.x.x or smt similar

[guosongjia]

Thanks for your kind help!\ I removed my old nextflow env, created a new one, and successfully deployed the software.\ The same results were generated using the example data with the following commands:\ nextflow run hoelzer/pocp -r 2.3.0 --proteins $HOME'/.nextflow/assets/hoelzer/pocp/example/*.faa' -profile local,conda\ Best,\ Guo-Song

[hoelzer]

Perfect. Thanks for the info!