New module: parsesdrf/convert

[jonasscheid]

Adds a new module sdrfpipelines/parsesdrf wrapping the parse_sdrf CLI from bigbio/sdrf-pipelines (bioconda sdrf-pipelines=0.1.3). The module converts an SDRF (Sample and Data Relationship Format) file into pipeline-specific samplesheets and search-preset files.
The conversion subcommand (e.g. convert-mhcquant, convert-openms) and its output flags are injected via task.ext.args rather than hardcoded, so the same module can serve different downstream proteomics pipelines. Pairs naturally with #11513

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[LouisLeNezet]

Hi,

Could you follow the nf-core convention with the meta map ?
This will allow to better control how the output tsv are named.

[LouisLeNezet]

As both output are expected they should be hardcoded in the script block.
Could you also use prefix = meta.id ?

[LouisLeNezet]

Please pass convert-mhcquant as params.module_args

[LouisLeNezet]

Also there is other files that can be passed to parse-sdrf could you add them as input ?
But after further reading it might be better to name the tool PARSESDRF_CONVERTMHCQUANT ?

[jonasscheid]

Thanks @LouisLeNezet for the hint, I initially wasn't sure how exactly to do it since the tool is very versatile, but I think you are right to rename to PARSESDRF_CONVERTMHCQUANT.

Edit: Should it be SDRFPIPELINES_CONVERTMHCQUANT or PARSESDRF_CONVERTMHCQUANT @LouisLeNezet 🤔

[LouisLeNezet]

Edit: Should it be SDRFPIPELINES_CONVERTMHCQUANT or PARSESDRF_CONVERTMHCQUANT

Good question 🤔

[jonasscheid]

Ok suggestion: Since CONVERTMHCQUANT is basically a pipeline specific module (local module), I guess it makes more sense to have a more generic nf-core module. Maybe makes more sense to cover e.g. the "convert-" subcommands (convert-openms, convert-mhcquant etc.) What do you think about SDRPIPELINES_CONVERT?

[LouisLeNezet]

What do you think about SDRPIPELINES_CONVERT?

I would agree at first thought, by adding a val(format), but I prefer to ask first other maintainers to be sure !

[LouisLeNezet]

After discussing with other maintainers, PARSESDRF_CONVERT might be best.
I have to admit that the people naming the package and tool could have choose only one 😄

[jonasscheid]

I have to admit that the people naming the package and tool could have choose only one 😄

💯 😄

Thanks for the effort! Really appreciated