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Use channel topic for tool versions #1109
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I think you managed to hit the small window when the MultiQC bioconda build was broken. If you try again now it should be fine 🤞🏻 |
This is awesome! Do you think it'd be possible to go even further and use a topic to pick up all of the MultiQC inputs, not just the versions? |
This is indeed awesome!! 🤩 When this is out in a release, we will first need to bump the minimum version of NF on nf-core/modules as well as in pipeline repos. Might need to delay a little to enable users to bump their NF version installs.
Presumably, you would need to explicitly add
Is it possible to use |
Okay I deleted the conda environment for multiqc but still got the error with a new build... does conda use a local cache that could be preventing a fresh download?
This will be the challenge. It might be better to only patch the nf-core modules for the rnaseq pipeline and update the modules after another stable release (or two).
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In any case, I tested rnaseq on master and it fails with the same error, so that at least makes me confident that there's no issue with the topic channels |
As for the multiqc inputs, a topic might not be the best choice because it is not obvious that the corresponding process outputs are intended solely for multiqc. For example, the
Some of these outputs are sent to multiqc, but you couldn't tell from the process definition. I think forcing a channel topic here would be more trouble than it's worth. |
Signed-off-by: Ben Sherman <[email protected]>
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Shall we move this forward? Channel topics are available in 23.11.0-edge. Let me know how you want to handle it. Or maybe someone from nf-core can take it forward, don't really need me anymore 😄
I was wrong about this, you can use Also would love to hear back about my comment regarding the use of |
Signed-off-by: Ben Sherman <[email protected]>
Signed-off-by: Ben Sherman <[email protected]>
I updated the CI and tests are passing now. The failing tests should work if they use 23.11.0-edge, but not sure how you wanted to manage that. |
This PR refactors the pipeline to use an experimental topic channel (nextflow-io/nextflow#4459) to collect the tool versions.
The topic channel works, but multiqc is failing with this error: