skewer.nf problem with Docker container.

[mbyott]

Description of the bug

Module compilation error
- file : /home/user/.nextflow/assets/nf-core/bacass/./workflows/../modules/local/skewer.nf
- cause: expecting '}', found ',' @ line 26, column 55.
                                 , emit: lo
                                 ^

1 error

Steps to reproduce

Steps to reproduce the behaviour:

1. Command line: nextflow run nf-core/bacass -r 2.0.0 -name amr_sample5 -profile docker -params-file nf-params.json

nf-params.json:

{
    "input": "amr_sample2.csv",
    "kraken2db": "\/home\/user\/minikraken2_v2_8GB_201904_UPDATE"
}

[d4straub]

Hm, I do not use -params-file routinely, but I did think it does not need those curly brackets? I thought it looks like described in https://nf-co.re/ampliseq/2.4.0/usage#setting-parameters-in-a-file? Could you test whether that solves your problem?

[mbyott]

Tried it and no joy. Unfortunately I also get the error when running the test command:

nextflow run nf-core/bacass -r 2.0.0 -profile test,docker

[d4straub]

I had success at least until SKEWER was finished with

nextflow run nf-core/bacass -r 2.0.0 -profile test,singularity
nextflow run nf-core/bacass -r 2.0.0 -profile test,docker

using N E X T F L O W ~ version 22.04.5, singularity version 3.7.0, and Docker version 20.10.7, build f0df350. Do you use an edge version of nextflow? If yes, use only stable releases. If no, probably pull the pipeline again? I.e. nextflow pull nf-core/bacass -r 2.0.0?