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edmundmiller
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Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 3.2.0. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
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let's merge #350 before |
bentsherman
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Jul 23, 2025
| Channel | ||
| .from(ch_input) | ||
| .splitCsv(header:false, sep:'', strip:true) | ||
| Channel.from(ch_input) |
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| Channel.from(ch_input) | |
| channel.of(ch_input) |
bentsherman
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Jul 23, 2025
| include { ASPERA_CLI } from '../../modules/local/aspera_cli' | ||
| include { SRA_TO_SAMPLESHEET } from '../../modules/local/sra_to_samplesheet' | ||
| include { softwareVersionsToYAML } from '../../subworkflows/nf-core/utils_nfcore_pipeline' | ||
| // TODO include { softwareVersionsToYAML } from 'plugin/nf-utils' |
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I think channel/operator logic should stay in the pipeline for now. Not sure yet if we should encourage people to hide it behind a plugin
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Gotcha. Would this be a good example of writing a function and using the map operator?
I think that'll definitely simplify the handling on my end. 😆
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You might be able to factor out some bits, like a function to transform the tuple (process, tool, version) into YAML. But the channel logic of merging the versions topic with legacy ch_versions would have to remain in the pipeline
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This will swap all of the functions and subworkflows into a plugin.
It should be much cleaner for updates from users.
Outstanding things to test(I'm just not a regular user of these features):
Things that still need fixing/re-working on nf-utils:
ERROR ~ The-profileoption cannot end with a trailing comma...workflow.onCompleteandworkflow.onErrorinto a traceObserver