hi all! i'm pretty new to nextflow and trying to get set up with nf-core/oncoanalyser for targeted sequencing with a custom panel but running into some problems when creating custom panel reference data files. after following the guide [here](oncoanalyser: Usage) and running the command, i get this error:

Error modules.config:314:128: Unexpected input: '='
 │ 314 | ame, "panel_resources/${filename}", panel_resource_creation = true) },
 ╰ | ^
 ERROR ~ Config parsing failed

i haven't found resources on what's causing this and how to get around this— wondering if anyone here is able to help. thanks in advance! edit: i ran

nextflow run nf-core/oncoanalyser -profile test,singularity --outdir results

to test my installation and got the same error; i don't know what could be causing this.

Hi @jasidhu, would you be able to send over the .nextflow.log?

This seems like a syntax error in

modules.config

, no? Simply having

true

(omitting function argument name) should fix this bug.

@Stephen Watts here is the log from running

nextflow run nf-core/oncoanalyser -profile test,singularity --outdir results

@Beatriz Sá Vinhas i haven't changed any of the config files that come with the pipeline but omitting the function argument name raises a similar error

Error modules.config:338:20: Unexpected input: '('
│ 338 | def get_saveas_path(meta, task, filename, path, panel_resource_creatio
╰     |                    ^
ERROR ~ Config parsing failed

could this be because nextflow strict syntax doesn't allow functions in config files [source]?

Thanks for the extra info, the error here seems to be caused by using Nextflow ≥26.04.0 as it has strict syntax enabled by default, which isn’t supported in the current oncoanalyser 2.3.0 release

Thank you @Stephen Watts!! Just a clarification @jasidhu: What I actually meant is that this is a bug in the code of

oncoanalyser

(which makes it not support strict syntax like @Stephen Watts mentioned), not in your config! 🙂

thank you stephen and beatriz!! switching to legacy syntax worked :)