Documentation udpate

tdayris · Jun 10, 2024 · ed7601b · ed7601b
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,3 +1,9 @@
+# 2.3.1
+
+## Features
+
+* Documentation udpate
+
 # 2.3.0
 
 ## Features

diff --git a/README.md b/README.md
@@ -43,6 +43,6 @@ The tools used in this pipeline are described [here](https://github.com/tdayris/
 
 | Step       | Wrapper                                                                                        |
 | ---------- | ---------------------------------------------------------------------------------------------- |
-| FastQC     | [fastqc-wrapper](https://snakemake-wrappers.readthedocs.io/en/v3.7.0/wrappers/fastqc.html)     |
-| FastScreen | [fastq-screen](https://snakemake-wrappers.readthedocs.io/en/v3.7.0/wrappers/fastq_screen.html) |
-| MultiQC    | [multiqc-wrapper](https://snakemake-wrappers.readthedocs.io/en/v3.7.0/wrappers/multiqc.html)   |
+| FastQC     | [fastqc-wrapper](https://snakemake-wrappers.readthedocs.io/en/v3.12.0/wrappers/fastqc.html)     |
+| FastScreen | [fastq-screen](https://snakemake-wrappers.readthedocs.io/en/v3.12.0/wrappers/fastq_screen.html) |
+| MultiQC    | [multiqc-wrapper](https://snakemake-wrappers.readthedocs.io/en/v3.12.0/wrappers/multiqc.html)   |
diff --git a/workflow/report/fastq_screen.rst b/workflow/report/fastq_screen.rst
@@ -2,4 +2,4 @@ This PNG_ image contains FastqScreen_ quality reports for sample {{ snakemake.wi
 It is a stand-alone file, and can be opened in your favorite web-browser.
 
 .. _PNG: https://en.wikipedia.org/wiki/PNG
-.. _FastqScreen: https://snakemake-wrappers.readthedocs.io/en/v3.10.2/wrappers/fastq_screen.html
+.. _FastqScreen: https://snakemake-wrappers.readthedocs.io/en/v3.12.0/wrappers/fastq_screen.html
diff --git a/workflow/report/fastqc.rst b/workflow/report/fastqc.rst
@@ -2,4 +2,4 @@ This HTML_ file contains FastQC_ quality reports for sample {{ snakemake.wildcar
 It is a stand-alone file, and can be opened in your favorite web-browser.
 
 .. _HTML: https://en.wikipedia.org/wiki/HTML
-.. _FastQC: https://snakemake-wrappers.readthedocs.io/en/v3.10.2/wrappers/fastqc.html
+.. _FastQC: https://snakemake-wrappers.readthedocs.io/en/v3.12.0/wrappers/fastqc.html
diff --git a/workflow/report/material_methods.rst b/workflow/report/material_methods.rst
@@ -13,12 +13,12 @@ whole pipeline was powered by Snakemake_ [#snakemakepaper]_.
 .. [#snakemakepaper] Köster, Johannes, and Sven Rahmann. "Snakemake—a scalable bioinformatics workflow engine." Bioinformatics 28.19 (2012): 2520-2522.
 
 
-.. _MultiQC: https://snakemake-wrappers.readthedocs.io/en/v3.10.2/wrappers/multiqc.html
+.. _MultiQC: https://snakemake-wrappers.readthedocs.io/en/v3.12.0/wrappers/multiqc.html
 .. _Snakemake: https://snakemake.readthedocs.io
 .. _Github: https://github.com/tdayris/fair_fastqc_multiqc
 .. _`Snakemake workflow`: https://snakemake.github.io/snakemake-workflow-catalog?usage=tdayris/fair_fastqc_multiqc
-.. _FastQC: https://snakemake-wrappers.readthedocs.io/en/v3.10.2/wrappers/fastqc.html
-.. _FastqScreen: https://snakemake-wrappers.readthedocs.io/en/v3.10.2/wrappers/fastq_screen.html
+.. _FastQC: https://snakemake-wrappers.readthedocs.io/en/v3.12.0/wrappers/fastqc.html
+.. _FastqScreen: https://snakemake-wrappers.readthedocs.io/en/v3.12.0/wrappers/fastq_screen.html
 
 
 :Authors:

diff --git a/workflow/report/multiqc.rst b/workflow/report/multiqc.rst
@@ -2,5 +2,5 @@ This HTML_ file contains quality reports of FastQC_ for all samples.
 It is a stand-alone file, and can be opened in your favorite `web-browser`_.
 
 .. _HTML: https://en.wikipedia.org/wiki/HTML
-.. _FastQC: https://snakemake-wrappers.readthedocs.io/en/v3.10.2/wrappers/fastqc.html
+.. _FastQC: https://snakemake-wrappers.readthedocs.io/en/v3.12.0/wrappers/fastqc.html
 .. _`web-browser`: https://en.wikipedia.org/wiki/Firefox