Updated some files for the 2.2.0 release

CHANGELOG.md

@@ -4,7 +4,47 @@ All notable changes to this project will be documented in this file.
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [2.2.Xdev] - 2024-0X-XX : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.2.X
+## [2.X.Xdev] - 2024-0X-XX : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.X.X
+
+### Credits
+
+Code contributions to the new version:
+
+### Template fixes and updates
+
+### Modules
+
+#### Added enhancements
+
+#### Fixes
+
+#### Changed
+
+#### Removed
+
+### Requirements
+
+## [2.X.Xhot] - 2024-0X-0X : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.X.1
+
+### Credits
+
+Code contributions to the hotfix:
+
+### Template fixes and updates
+
+### Modules
+
+#### Added enhancements
+
+#### Fixes
+
+#### Changed
+
+#### Removed
+
+### Requirements
+
+## [2.2.0] - 2024-09-12 : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.2.0
 
 ### Credits
 
@@ -70,6 +110,7 @@ Code contributions to the new version:
 - Updated several templates (singularity images, outdated paths, improvements, etc) [#331](https://github.com/BU-ISCIII/buisciii-tools/pull/331)
 - Added permissions fixing after running scratch_copy, as well as a new fix-permissions module in the tools [#332](https://github.com/BU-ISCIII/buisciii-tools/pull/332).
 - Updated MAG lablogs and utils.py [#334](https://github.com/BU-ISCIII/buisciii-tools/pull/334).
+- Updated some files (setup.py, __main__.py, README, etc) for the 2.2.0 release [#335](https://github.com/BU-ISCIII/buisciii-tools/pull/335).
 
 ### Modules
 
@@ -96,26 +137,6 @@ Code contributions to the new version:
 
 ### Requirements
 
-## [2.X.1hot] - 2024-0X-0X : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.X.1
-
-### Credits
-
-Code contributions to the hotfix:
-
-### Template fixes and updates
-
-### Modules
-
-#### Added enhancements
-
-#### Fixes
-
-#### Changed
-
-#### Removed
-
-### Requirements
-
 ## [2.1.0] - 2024-04-19 : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.1.0
 
 ### Credits

README.md

@@ -21,6 +21,7 @@ BU-ISCIII provides a serie or services in its portfolio for supporting bioinform
       - [bioinfo\_doc](#bioinfo_doc)
       - [archive](#archive)
       - [autoclean\_sftp](#autoclean_sftp)
+      - [fix-permissions](#fix-permissions)
   - [Acknowledgements](#acknowledgements)
 
 ## Installation
@@ -94,6 +95,8 @@ Commands:
   finish       Service cleaning, remove big files, rename folders before...
   bioinfo-doc  Create the folder documentation structure in bioinfo_doc...
   archive      Archive services or retrieve services from archive
+  autoclean-sftp   Clean old sftp services
+  fix-permissions  Fix permissions
 ```
 
 #### list
@@ -389,6 +392,26 @@ Options:
   --help                  Show this message and exit.
 ```
 
+#### fix-permissions
+
+Example of usage:
+
+```bash
+bu-isciii fix-permissions -d /data/bi
+```
+
+Help:
+
+```bash
+Usage: bu-isciii fix-permissions [OPTIONS]
+
+  Fix permissions
+
+Options:
+  -d, --input_directory PATH  Input directory to fix permissions (absolute path) [required]
+  --help                  Show this message and exit.
+```
+
 ## Acknowledgements
 
 Python package idea and design is really inspired in [nf-core/tools](https://github.com/nf-core/tools).

bu_isciii/__main__.py

@@ -57,7 +57,7 @@ def run_bu_isciii():
     )
 
     # stderr.print("[green]                                          `._,._,'\n", highlight=False)
-    __version__ = "2.1.0"
+    __version__ = "2.2.0"
     stderr.print(
         "[grey39]    BU-ISCIII-tools version {}".format(__version__), highlight=False
     )

bu_isciii/bioinfo_doc.py

@@ -187,6 +187,7 @@ def __init__(
         self.samples = self.resolution_info.get("samples", None)
         self.versions = self.load_versions()
         self.handled_services = None
+        self.all_services = None
         try:
             self.config_pdfkit = pdfkit.configuration()
         except OSError as e:

bu_isciii/templates/viralrecon/ANALYSIS/remove_columns_mapping_table.sh

@@ -3,7 +3,8 @@
 output_file=$(echo processed_mapping_illumina_$(date '+%Y%m%d').tab)
 
 # Removal of the first three columns of the mapping illumina tab file
-cut --complement -f1-3 *.tab > output_file
+cut --complement -f1-3 mapping_*.tab > output_file
+mv $output_file mapping_illumina_$(date '+%Y%m%d').tab
 
 # Success message
 if [ $? -eq 0 ]; then

setup.py

@@ -2,7 +2,7 @@
 
 from setuptools import setup, find_packages
 
-version = "2.1.0"
+version = "2.2.0"
 
 with open("README.md") as f:
     readme = f.read()