Add Hello nf-core training course #610
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kenibrewer
reviewed
May 13, 2025
| 2. Select **Custom** on the `Choose pipeline type` screen | ||
| 3. Enter your pipeline details, replacing < YOUR NAME > with your own name, then select **Next** | ||
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| **GitHub organisation:** core |
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| **GitHub organisation:** core | |
| **GitHub organisation:** core (or your github username) |
kenibrewer
reviewed
May 14, 2025
| Believe it or not, even though you haven't yet added any modules to make it do real work, the pipeline scaffold can actually be run using the test profile, the same way we ran the `nf-core/demo` pipeline. | ||
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| ```bash | ||
| nextflow run core-hello -profile docker,test --outdir core-hello-results |
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| nextflow run core-hello -profile docker,test --outdir core-hello-results | |
| nextflow run ./core-hello -profile docker,test --outdir core-hello-results |
For some additional clarity vs nextflow run hello
kenibrewer
reviewed
May 14, 2025
| We finally have all the pieces we need to verify that the composable workflow works. | ||
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| ```bash | ||
| nextflow run original-hello |
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| nextflow run original-hello | |
| nextflow run ./original-hello |
kenibrewer
approved these changes
May 14, 2025
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| final_result = cowpy.out |
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| final_result = cowpy.out | |
| cowpy_hellos = cowpy.out |
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| ```groovy title="original-hello/hello.nf" linenums="37" | ||
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| final_result = cowpy.out |
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| final_result = cowpy.out | |
| cowpy_hellos = cowpy.out |
| cowpy(collectGreetings.out.outfile, params.character) | ||
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| ```groovy title="core-hello/workflows/hello.nf" linenums="55" hl_lines="2" | ||
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| final_result = cowpy.out | |
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| cowpy(collectGreetings.out.outfile, params.character) | ||
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| However, you do need a (free) GitHub account to log in, and you should take a few minutes to familiarize yourself with the interface. | ||
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| If you have not yet done so, please go through the [Environment Setup](../../envsetup/) mini-course before going any further. | ||
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| !!! warning | |
| This training is designed for nf-core tools version 3.2.1, which should be the version installed in the codespace. If you use a different version of nf-core tooling you may have difficulty following along. | |
| You can check what version is installed using the command`nf-core --version`. | |
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This converts and expands the nf-core side quest (originally written from material by @christopher-hakkaart and further expanded by @FriederikeHanssen) into a proper training course of its own, similar in spirit to the Hello Nextflow training course.
Addresses #546
There are 3 main training sections:
Current status:
"Add an existing nf-core module" will be added in a followup