Merge branch 'dataintegrity' into 'master'

Update to v3.1.0

See merge request bioinfo/SAMBA-nextflow!10

.gitignore

@@ -6,3 +6,5 @@ training_dataset/
 runSAMBA_test.o*
 results
 work
+.idea/
+containers/*.img

CHANGELOG.md

@@ -1,23 +1,18 @@
 # samba: Changelog
 
-The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
-and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
+## v3.1.0 - November 2022
 
-## v3.0.0 - January 2021
-
-This release integrates the analysis of long reads data. The pipeline has also been incremented with new steps to provide a multitude of options to users (interactive figures, taxonomic filter, ...)
+This release integrates the use of an XLS file (EXCEL 97-2004) as input by converting automatically in manifest and metadata file. 
 
 ### `Added`
 
-* Long read processing
-* Filter based on taxonomic assignation
-* Automated unwanted sample removal
+* excel2tsv process
 
 ### `Fixed`
 
 ### `Dependencies`
 
-See README.md
+* Update Biopython version to 1.79
 
 ### `Deprecated`
 

README.md

@@ -1,6 +1,6 @@
 # **SAMBA: Standardized and Automated MetaBarcoding Analyses workflow**.
 
-[![SAMBA version](https://img.shields.io/badge/samba%20version-v3.0.2-red?labelColor=000000)](https://www.nextflow.io/)
+[![SAMBA version](https://img.shields.io/badge/samba%20version-v3.1.0-red?labelColor=000000)](https://www.nextflow.io/)
 [![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A519.10.0-23aa62.svg?labelColor=000000)](https://www.nextflow.io/)
 [![Run with with conda](https://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![Run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)

assets/template.html

@@ -85,7 +85,9 @@
                         {% if d.steps.picrust2_enable == 'true' %}
                             <li><a href="#picrsut">Functional predictions</a></li>
                         {% endif %}
+                        {% if d.steps.ancom_enable == 'true' %}
                         <li><a href="#ancom">Differential abundance</a></li>
+                        {% endif %}
                         <li><a href="#final-output">Final outputs</a></li>
                     {% else %}
                         <li><a href="#taxo-assign">Taxonomic assignation</a></li>