A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

<!here> the first batch of module updates with versions outputs using topic channels are about to be merged. Please make sure your pipeline is using the latest template when updating modules so your pipeline still correctly handles the versions. I will do a bytesize about this next week so stay tuned :wink:

Wait ... you will do this for all modules?

Yes all modules will be migrated in time. This will however take some time

The template is able to handle both methods so the migration should be trivial if you are using the latest template

Thanks for making the effort!, I thought people feeling responsible for individual modules would do that

It will be a community effort, for now the linting warns when topics are not part of a module but this will fail in the next version of nf-core/tools. So people will be forced to migrate next year

These are mainly the modules we converted during the hackathon now :slightly_smiling_face:

I'm still reading up on what all of this entails, so apologies if I'm missing something obvious, but updating the fastqc module to the most recent version, after updating to the latest nf-core tool template, causes some problems for me.

I.e. I had to manually remove _`ch_versions = ch_versions.mix(FASTQC.out.versions.first())` ._  And the version of fastqc is not showing up in my multiqc output yet, but it is showing in the `pipeline_info` folder.

Yes that manual removal is something you should do yourself, but that's not too much work. For the versions not showing up in multiqc is weird because multiqc uses that file in pipeline_info :thinking_face:

I'll play around it with it some more and get back to you. Happy to hear that that removal still needs to happen, I was afraid I'd messed up my template updates :neutral_face:

Thank you let me know if you know more. I'll take a look at it too whenever I find some time

Have you checked if the template merge has happened correctly? I've noticed some merges have the `softwareVersionsToYaml` function twice where the latter one overwrites the first one

Just tried with a brand new template pipeline (`nf-core pipelines create --name testpipeline --description "short description" --author testauthor --outdir testpipeline --organisation testorg`) where I updated the fastqc module from `41dfa` to `0b243` .

`ERROR ~ No such variable: Exception evaluating property 'versions' for nextflow.script.ChannelOut, Reason: groovy.lang.MissingPropertyException: No such property: versions for class: groovyx.gpars.dataflow.DataflowBroadcast`

After commenting the line: `ch_versions = ch_versions.mix(FASTQC.out.versions.first())`  everything appears to work, `testpipeline_software_mqc_versions.yml` contains fastqc 0.12.1, as does the multiqc_report.html.

After rerunning my own pipeline, the versions are showing up correctly everywhere as well now. So all is good as long as that ch_versions.mix line is removed. Thanks for checking :slightly_smiling_face: