From 592c84ff1cbab15f3c6edd07516607e989dc8425 Mon Sep 17 00:00:00 2001 From: Lilferrit Date: Thu, 10 Oct 2024 14:16:40 -0700 Subject: [PATCH 1/5] nextflow documentation --- docs/index.md | 1 + docs/nextflow.md | 5 +++++ 2 files changed, 6 insertions(+) create mode 100644 docs/nextflow.md diff --git a/docs/index.md b/docs/index.md index f0c5700f..97a10325 100644 --- a/docs/index.md +++ b/docs/index.md @@ -17,6 +17,7 @@ maxdepth: 1 Getting Started File Formats Command Line Interface +Casanovo Nextflow Workflow FAQs Contributing Code of Conduct diff --git a/docs/nextflow.md b/docs/nextflow.md new file mode 100644 index 00000000..f8c44e27 --- /dev/null +++ b/docs/nextflow.md @@ -0,0 +1,5 @@ +# Casanovo Nextflow Workflow + +To simplify the process of setting up and running Casanovo, a dedicated Nextflow workflow is available. +This Casanovo Nextflow workflow automates the installation and execution of Casanovo and its dependencies. +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 From 179b03b8e30c24746d47f18037507c027b07b674 Mon Sep 17 00:00:00 2001 From: Lilferrit Date: Tue, 15 Oct 2024 16:22:27 -0700 Subject: [PATCH 2/5] nextflow nav prefix, more nextflow docs details --- docs/index.md | 2 +- docs/nextflow.md | 5 +++-- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/docs/index.md b/docs/index.md index 97a10325..130e7cfa 100644 --- a/docs/index.md +++ b/docs/index.md @@ -17,7 +17,7 @@ maxdepth: 1 Getting Started File Formats Command Line Interface -Casanovo Nextflow Workflow +Nextflow Workflow FAQs Contributing Code of Conduct diff --git a/docs/nextflow.md b/docs/nextflow.md index f8c44e27..2fc3837d 100644 --- a/docs/nextflow.md +++ b/docs/nextflow.md @@ -1,5 +1,6 @@ # Casanovo Nextflow Workflow -To simplify the process of setting up and running Casanovo, a dedicated Nextflow workflow is available. -This Casanovo Nextflow workflow automates the installation and execution of Casanovo and its dependencies. +To simplify the process of setting up and running Casanovo, a dedicated [Nextflow](https://www.nextflow.io/) workflow is available. +In addition to automatic 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://bioinformaticshome.com/tools/proteomics/descriptions/msconvert.html#gsc.tab=0), 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 may be ran 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 From f6a7c74493c1699b5682a52207adac74529ac4a0 Mon Sep 17 00:00:00 2001 From: Lilferrit Date: Mon, 21 Oct 2024 15:59:28 -0700 Subject: [PATCH 3/5] grammatical fixes --- docs/nextflow.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/nextflow.md b/docs/nextflow.md index 2fc3837d..33de2f46 100644 --- a/docs/nextflow.md +++ b/docs/nextflow.md @@ -1,6 +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 automatic 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://bioinformaticshome.com/tools/proteomics/descriptions/msconvert.html#gsc.tab=0), 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 may be ran on POSIX-compatible (UNIX) systems, Windows using WSL, or on a cloud platform such as AWS. +To simplify the process of setting up and running Casanovo, a dedicated [Nextflow](https://proteowizard.sourceforge.io/tools/msconvert.html) 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://bioinformaticshome.com/tools/proteomics/descriptions/msconvert.html#gsc.tab=0), 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 From 5c77436b567c38810ad42c2cf9ea0311f44f31cf Mon Sep 17 00:00:00 2001 From: Lilferrit Date: Tue, 22 Oct 2024 17:00:53 -0700 Subject: [PATCH 4/5] grammatical fixes --- docs/nextflow.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/nextflow.md b/docs/nextflow.md index 33de2f46..7104ece3 100644 --- a/docs/nextflow.md +++ b/docs/nextflow.md @@ -1,6 +1,6 @@ # Casanovo Nextflow Workflow To simplify the process of setting up and running Casanovo, a dedicated [Nextflow](https://proteowizard.sourceforge.io/tools/msconvert.html) 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://bioinformaticshome.com/tools/proteomics/descriptions/msconvert.html#gsc.tab=0), infers peptide sequences using Casanovo, and (optionally) uploads the results to [Limelight](https://limelight-ms.org/) - a platform for sharing and visualizing proteomics results. +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://bioinformaticshome.com/tools/proteomics/descriptions/msconvert.html#gsc.tab=0), 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 From 0634f90b3f61bd277d67b217c403e6d686af4586 Mon Sep 17 00:00:00 2001 From: Lilferrit Date: Tue, 29 Oct 2024 16:46:59 -0700 Subject: [PATCH 5/5] fixed links --- docs/nextflow.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/nextflow.md b/docs/nextflow.md index 7104ece3..b459e40e 100644 --- a/docs/nextflow.md +++ b/docs/nextflow.md @@ -1,6 +1,6 @@ # Casanovo Nextflow Workflow -To simplify the process of setting up and running Casanovo, a dedicated [Nextflow](https://proteowizard.sourceforge.io/tools/msconvert.html) 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://bioinformaticshome.com/tools/proteomics/descriptions/msconvert.html#gsc.tab=0), infers peptide sequences using Casanovo, and (optionally) uploads the results to [Limelight](https://limelight-ms.org/) - a platform for sharing and visualizing proteomics results. +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