From ed7601b52fd31b02897b1e42535a007ce827b73a Mon Sep 17 00:00:00 2001 From: tdayris Date: Mon, 10 Jun 2024 09:03:19 +0200 Subject: [PATCH] Documentation udpate --- CHANGELOG.md | 6 ++++++ README.md | 6 +++--- workflow/report/fastq_screen.rst | 2 +- workflow/report/fastqc.rst | 2 +- workflow/report/material_methods.rst | 6 +++--- workflow/report/multiqc.rst | 2 +- 6 files changed, 15 insertions(+), 9 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index d726ca1..31feba5 100644 --- 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 index bfaace3..21b1f1a 100644 --- 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 index 27a59e4..26c2bd9 100644 --- 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 index b0d3e83..d30faa6 100644 --- 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 index 8502dee..0005acc 100644 --- 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 index 84a8bf4..79e8ff0 100644 --- 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