From 4eb9d99ad0701eede8360e03f6f6c237d7dc7821 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Tue, 19 Nov 2024 18:07:58 +0000 Subject: [PATCH] Correct hangover from before we added all the script: --- docs/hello_nextflow/05_hello_operators.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/docs/hello_nextflow/05_hello_operators.md b/docs/hello_nextflow/05_hello_operators.md index 5ee507c0..0fdf4a1f 100644 --- a/docs/hello_nextflow/05_hello_operators.md +++ b/docs/hello_nextflow/05_hello_operators.md @@ -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} \