New module: Seqera Platform CLI

[vladsavelyev]

Parses runs_*.tar.gz dumps containing logs and stats from a Seqera Platform run. To be triggered in the https://github.com/seqeralabs/nf-aggregate workflow, or can parse the output of tw runs dump ... --output=runs_SmUkr43Nul49G.tar.gz directly.

Note that binary files by default are ignored by MultiQC, so you need to set ignore_images: false in the MultiQC config to make it parse the input tar-gz file. This can be done via the CLI:

multiqc -m seqera_cli test_data/data/modules/seqera_cli -f -v --cl-config "ignore_images: false"

• Think what general stats cols to hide?
• Figure out how to better present start date/end date
• Test with many runs
• Add a bar plot with a category per status of workflows/processs?

[ewels]

Given that the tar step is from the workflow and not from the Seqera CLI itself, I think we should also cater for uncompressed files. Then can handle the custom stuff in the pipeline but it stays as general use as possible.

[drpatelh]

The Seqera CLI natively dumps tar files. I was going to uncompress them in the same process that dumps the run info but if we don't have to then that would be a bonus. Supporting both would be great. The JSON files all have standard names so will be easy to scrape if we stage each run in its individual directory / archive.

[github-actions]

🚀 Deployed on https://mqc-pr-2151--multiqc.netlify.app

[vladsavelyev]

Added support for both compressed and uncompressed dumps. Also added a barplot and parsing of the platform version.

[ewels]

Figure out how to better present start date/end date

Maybe show a duration as a column, keep start + end dates but hide by default.

[ewels]

👉🏻 Should specify the task status order + colours in the bar plot to match Tower:

• Pending: #8f4199
• Submitted: #e68642
• Running: #4256e7
• Cached: #939598
• Succeeded: #28ae61
• Failed: #e7363e

[vladsavelyev]

Updates:

• Using a shorter repositroy names to display,
• Using the Tower color code for process status, as Phil proposed,
• Hiding start/end and showing duration by default.
• For time stamps, dates, and gigabytes, we want a human-readable representation, but still sorting abilities. I added support for the format key to be a lambda function, so we can use arbitrary code there instead of a format string. I also modified the plotting code to add a val= attribute into dt table cells containing the original sortable floating value (i.e. for time stamps, that would be the number of sections), and modified the JavaScript table sorting code to take that val into account before using innerText.

[ewels]

Minor comments, otherwise LGTM!

[ewels]

LGTM to me to merge, waiting on review from @drpatelh before hitting the button.

[ewels]

Suggestion: Move CPU time and Cost columns up, alongside pipeline duration. These 3 columns are likely typically the most interesting.

[robsyme]

We know that cpuEfficiency and memoryEfficiency will always be percentages, so should format as such.

[drpatelh]

Great! Can we put the Nextflow entry before the Platform one please?

[vladsavelyev]

Done! (updated the comment above)

[drpatelh]

Beautiful! Last main thing to add would be the Plots I outlined in #2151 (comment)

Copied again below:

Additional Plots

It would be great to at least have bar plots for the more pertinent metrics so they can be dumped directly into presentations if required rather than having to generate them via another tool:

• CPU Time
• Wall Time
• Estimated cost ($)

I have created issues on the Seqera CLI for things that would be good to add in the future. For now, I can try to find a workaround for using run names in the plots via a mapping file.

[vladsavelyev]

It would be great to at least have bar plots for the more pertinent metrics so they can be dumped directly into presentations if required rather than having to generate them via another tool:

I'm not sure I understand though what would be the categories in such bar plots. In the dump, there is only one value per run, which fits a table column - which translates into a simple bar plot by the means of the background color bar:

But that doesn't fit a bar plot, where you want multiple non-overlapping categories that can sum up.

If we had per-process numbers, that might work - we could use the N heaviest processes as categories, plus "the remaining" as the last tail category.

[drpatelh]

We would have a separate plot for each metric which should be relatively simple? Definitely don't want to put those all in the same plot.

[vladsavelyev]

Such a plot for a single-value metric would just duplicate the corresponding table column.

Is this something that you have in mind?

We do have this plot in the table already:

[drpatelh]

Yes, exactly! One for each of the metrics I listed. The problem with having that in the table is you can't export it as a plot. Also, it will be nice to bring a larger focus on the core metrics if we have individual plots.

[vladsavelyev]

Alright, let's add those. It would be nice to add per-process data into the run dump though, to make the bars more informative.

multiqc_report.html.zip

[drpatelh]

Looks awesome @vladsavelyev ! 🤩 Thank you! Some minor comments for consistency but otherwise LGTM! Be great to add in some other things in the future but this is definitely a good start.

[ewels]

Looks great! 👏🏻