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✨ Add post-run scripts note #28

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merged 2 commits into from
May 1, 2024
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✨ Add post-run scripts note #28

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bbcdb28
:sparkles: Add post-run scripts note
Zethson May 1, 2024
7d34bc1
:art: Address some more feedback
Zethson May 1, 2024
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26 changes: 7 additions & 19 deletions docs/mcmicro_02.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -25,19 +25,11 @@
"source": [
"```{note}\n",
"\n",
"This notebook serves as a demo for how to integrate lamindb with Nextflow runs.\n",
"Typically, you run the Nextflow workflow from the command line or Nextflow tower and then register input and output data with a script.\n",
"Typically, you run the Nextflow workflow from the command line or Seqera Platform and then register input and output data with a script.\n",
"The Seqera Platform allows for [post-run scripts](https://docs.seqera.io/platform/23.4.0/launch/advanced#pre-and-post-run-scripts) that can automate this process.\n",
"```"
]
},
{
"cell_type": "markdown",
"id": "fe9ab200",
"metadata": {},
"source": [
"## Setup"
]
},
{
"cell_type": "markdown",
"id": "b7c8e52d",
Expand Down Expand Up @@ -104,7 +96,11 @@
"cell_type": "code",
"execution_count": null,
"id": "38e83af2",
"metadata": {},
"metadata": {
"tags": [
"hide-output"
]
},
"outputs": [],
"source": [
"!python register_mcmicro_run.py"
Expand Down Expand Up @@ -185,14 +181,6 @@
"source": [
"!lamin delete --force nextflow-mcmicro"
]
},
{
"cell_type": "markdown",
"id": "ce3e6e84",
"metadata": {},
"source": [
"If you are interested in registering bulk RNA-seq data with Lamin, you can have a look at our [nf-core/rnaseq example](https://github.com/laminlabs/nextflow-lamin-usecases/blob/main/nextflow_bulk_rna.ipynb)."
]
}
],
"metadata": {
Expand Down
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