Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Casanovo Nextflow Workflow Documentation #391

Merged
merged 5 commits into from
Oct 30, 2024
Merged

Casanovo Nextflow Workflow Documentation #391

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
592c84f
nextflow documentation
Lilferrit Oct 10, 2024
179b03b
nextflow nav prefix, more nextflow docs details
Lilferrit Oct 15, 2024
f6a7c74
grammatical fixes
Lilferrit Oct 21, 2024
5c77436
grammatical fixes
Lilferrit Oct 23, 2024
0634f90
fixed links
Lilferrit Oct 29, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions docs/index.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,7 @@ maxdepth: 1
Getting Started <getting_started.md>
File Formats <file_formats.md>
Command Line Interface <cli.rst>
Nextflow Workflow <nextflow.md>
FAQs <faq.md>
Contributing <CONTRIBUTING.md>
Code of Conduct <CODE_OF_CONDUCT.md>
Expand Down
6 changes: 6 additions & 0 deletions docs/nextflow.md
View file
Open in desktop
bittremieux marked this conversation as resolved.
Show resolved Hide resolved
Original file line number Diff line number Diff line change
@@ -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/#).
Loading