From e2290fa35b19531a266dd15ceffa28b099b210c9 Mon Sep 17 00:00:00 2001 From: Gwenneth Straub Date: Wed, 30 Oct 2024 01:19:14 -0700 Subject: [PATCH] Casanovo Nextflow Workflow Documentation (#391) * nextflow documentation * nextflow nav prefix, more nextflow docs details * grammatical fixes * grammatical fixes * fixed links --- docs/index.md | 1 + docs/nextflow.md | 6 ++++++ 2 files changed, 7 insertions(+) create mode 100644 docs/nextflow.md diff --git a/docs/index.md b/docs/index.md index f0c5700f..130e7cfa 100644 --- a/docs/index.md +++ b/docs/index.md @@ -17,6 +17,7 @@ maxdepth: 1 Getting Started File Formats Command Line Interface +Nextflow Workflow FAQs Contributing Code of Conduct diff --git a/docs/nextflow.md b/docs/nextflow.md new file mode 100644 index 00000000..b459e40e --- /dev/null +++ b/docs/nextflow.md @@ -0,0 +1,6 @@ +# Casanovo Nextflow Workflow + +To simplify the process of setting up and running Casanovo, a dedicated [Nextflow](https://www.nextflow.io/) workflow is available. +In addition to simplifying the installation of Casanovo and its dependencies, the Casanovo Nextflow workflow provides an automated mass spectrometry data pipeline that converts input data files to a Casanovo-compatible format using [msconvert](https://proteowizard.sourceforge.io/tools/msconvert.html), infers peptide sequences using Casanovo, and (optionally) uploads the results to [Limelight](https://limelight-ms.org/) - a platform for sharing and visualizing proteomics results. +The workflow can be used on POSIX-compatible (UNIX) systems, Windows using WSL, or on a cloud platform such as AWS. +For more details, refer to the [Casanovo Nextflow Workflow Documentation](https://nf-ms-dda-casanovo.readthedocs.io/en/latest/#). \ No newline at end of file