Aws fix

[Deriverx2]

PR checklist

The error is from not having the following file 'conf/aws/batch/nextflow.config' mentinoined in nextflow.config in nf-core/methylseq line 251

    aws_batch       { includeConfig 'conf/aws/batch/nextflow.config' }

So The only way to get rid of it is by adding that file, and while patching that I also came across this:

 tuple val(meta), env(trim_OT), env(trim_OB),                    emit: mbias_processed_str

The env variables are not supposed to be defined like that.

NOTE: This is just a temporary patch
This passes nextflow run . -profile test,docker --outdir and have also been checked in debug mode.

[nf-core-bot]

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.5.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

[eduard-watchmaker]

good catch!

[eduard-watchmaker]

@nf-core-bot fix linting

[eduard-watchmaker]

Sorry module changes need to be done in nf-core/modules, see here:

https://github.com/nf-core/modules/blob/master/modules/nf-core/rastair/mbiasparser/main.nf

[eduard-watchmaker]

@nf-core-bot fix linting

[eduard-watchmaker]

Hum this is the error I see when linting, it should be irrelevant to this PR:

╭─ [!] 1 Pipeline Test Warning ────────────────────────────────────────────────╮
│ │
│ local_component_structure: filter_bedgraph_targets.nf in modules/local │
│ should be moved to a TOOL/SUBTOOL/main.nf structure │
│ │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ [✗] 1 Pipeline Test Failed ─────────────────────────────────────────────────╮
│ │
│ nextflow_config: Plugin 'nf-amazon' does not have a pinned version │
│ │
╰──────────────────────────────────────────────────────────────────────────────╯

[Deriverx2]

@eduard-watchmaker The variables should be exported to get the values right? It seems you have removed the export keyword.
Should I make it similar to: https://github.com/nf-core/modules/blob/master/modules/nf-core/rastair/mbiasparser/main.nf

[eduard-watchmaker]

@eduard-watchmaker The variables should be exported to get the values right? It seems you have removed the export keyword. Should I make it similar to: https://github.com/nf-core/modules/blob/master/modules/nf-core/rastair/mbiasparser/main.nf

I think the export should be there in the rastair/mbiasparser module in nf-core/modules ? Maybe you just need to install / update the rastair modules in your pipeline using the nf-core toolkit?

[Deriverx2]

Great. Updating the rastair/mbiasparser module

nf-core modules update rastair/mbiasparser

fixes it. So this will be incorporated into the next update right?

Is there anything I can do to help.