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codeisscience / software-usage-reporting

Tiered software usage reporting recommendations from #BOSC2019
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review nf-core report formats #2

Open mr-c opened 4 years ago

mr-c commented 4 years ago

The following is courtesy @heuermh

In nf-core, it is a best-practice (and generated by the nf-core getting-started template) to capture software versions

https://github.com/nf-core/rnaseq/blob/09e8214704d81332ad1c391dc8d72f801c8def23/main.nf#L370

echo $workflow.manifest.version &> v_ngi_rnaseq.txt
echo $workflow.nextflow.version &> v_nextflow.txt
fastqc --version &> v_fastqc.txt
scrape_software_versions.py &> software_versions_mqc.yaml

I'm not confidently sure how this file is used … looks like the multiqc tool may use it to generate an HTML report?

https://github.com/nf-core/rnaseq/blob/09e8214704d81332ad1c391dc8d72f801c8def23/main.nf#L1318

file ('software_versions/*') from software_versions_yaml.collect()

ewels commented 4 years ago

Hi all!

@huermh has pretty much all of it from the nf-core side - this is a “custom content” file for MultiQC, basically some HTML with a bit of meta that gets plonked into the base of the report.

This code is in the main nf-core template, so should be present in all nf-core pipelines. If we can update it to be better (eg. additional output files in a standard format) then we’d certainly be interested! It should be fairly easy for us to implement..

Phil

ewels commented 4 years ago

ps. This is nf-core pipelines only and not all of nextflow. I have talked to @pditommaso about ideas for building core nextflow features around this ages ago, but it hasn’t gone anywhere (yet). See https://github.com/nextflow-io/nextflow/issues/879