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Merge pull request #467 from nextflow-io/script_hangover
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Correct hangover from before we added all the script:
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pinin4fjords authored Nov 19, 2024
2 parents 2768c4f + 4eb9d99 commit 314bd4e
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5 changes: 3 additions & 2 deletions docs/hello_nextflow/05_hello_operators.md
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Expand Up @@ -582,14 +582,15 @@ That is because Nextflow must see them as file paths in order to stage the files

But _where_ in the process can we add this?

Fun fact, if you add the optional reserved keyword `script:` before the `"""` that starts the bash scripting block, you can add arbitrary code in there!
Fun fact: you can add arbitrary code after `script:` and before the `"""` !

Great, let's add the `script:` keyword and string manipulation line there then, and update the `gatk GenomicsDBImport` command to use the concatenated string it produces.
Great, let's add our string manipulation line there then, and update the `gatk GenomicsDBImport` command to use the concatenated string it produces.

_Before:_

```groovy title="hello-operators.nf" linenums="87"
"""
script:
gatk GenomicsDBImport \
-V ${all_gvcfs} \
-L ${interval_list} \
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