Merge changes from main into hotfix

.github/workflows/python_lint.yml

@@ -14,7 +14,7 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v1
         with:
-          python-version: 3.9.x
+          python-version: 3.10.x
           architecture: x64
       - name: Checkout PyTorch
         uses: actions/checkout@v2

README.md

@@ -69,13 +69,13 @@ pip install .
 Run bu-isciii tools:
 
 ```bash
-bu-isciii --help
+buisciii --help
 ```
 
 Outputs the following:
 
 ```bash
-Usage: bu-isciii [OPTIONS] COMMAND [ARGS]...
+Usage: buisciii [OPTIONS] COMMAND [ARGS]...
 
 Options:
   --version                  Show the version and exit.
@@ -84,7 +84,9 @@ Options:
   -u, --api_user TEXT        User for the API logging
   -p, --api_password TEXT    Password for the API logging
   -c, --cred_file TEXT       Config file with API logging credentials
-  --help                     Show this message and exit
+  -D, --debug                Show the full traceback on error for debugging purposes.
+  -d, --dev                  Develop settings
+  --help                     Show this message and exit.
 
 Commands:
   list         List available bu-isciii services.
@@ -110,7 +112,7 @@ bu-isciii list
 Help:
 
 ```bash
-Usage: bu-isciii list [OPTIONS] <service>
+Usage: buisciii list [OPTIONS] <service>
 
   List available bu-isciii services.
 
@@ -121,55 +123,43 @@ Options:
 Output:
 
 ```bash
-┏━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
-┃           Service name ┃ Description                               ┃ Github                                     ┃
-┡━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩
-│    assembly_annotation │ Nextflow assembly pipeline to assemble    │ https://github.com/Daniel-VM/bacass/...    │
-│                        │ bacterial genomes                         │                                            │
-│        mtbseq_assembly │ Mycobacterium tuberculosis mapping,       │ https://github.com/ngs-fzb/MTBseq_source   │
-│                        │ variant calling and detection of          │                                            │
-│                        │ resistance using MTBseq                   │                                            │
-│                 mtbseq │ Mycobacterium tuberculosis mapping,       │ https://github.com/ngs-fzb/MTBseq_source   │
-│                        │ variant calling and detection of          │                                            │
-│                        │ resistance using MTBseq                   │                                            │
-│              pikavirus │ PikaVirus, a mapping-based tool for       │ https://github.com/BU-ISCIII/PikaVirus     │
-│                        │ metagenome analysis of virus.             │                                            │
-│     plasmidid_assembly │ Plasmid identification tool based on      │ https://github.com/BU-ISCIII/plasmidID     │
-│                        │ mapping and assisted by assembly          │                                            │
-│         wgmlst_taranis │ Multilocus sequence typing (MLST) using   │ https://github.com/BU-ISCIII/taranis       │
-│                        │ Taranis                                   │                                            │
-│       wgmlst_chewbbaca │ Multilocus sequence typing (MLST) using   │ https://github.com/B-UMMI/chewBBACA        │
-│                        │ chewBBACA                                 │                                            │
-│             viralrecon │ Viral genome reconstruction analysis for  │ https://github.com/BU-ISCIII/viralrecon    │
-│                        │ SARS-COV-2 data                           │                                            │
-│                 rnaseq │ RNA-seq analysis                          │ https://github.com/nf-core/rnaseq          │
-│          lowfreq_panel │ Low frequency variant calling from        │                                            │
-│                        │ enrichment panel.                         │                                            │
-│                 snippy │ Rapid haploid variant calling and core    │ https://github.com/tseemann/snippy         │
-│                        │ genome alignment                          │                                            │
-│       seek_and_destroy │ Simple pipeline for basic quality         │ https://github.com/GuilleGorines/Seek-Des… │
-│                        │ control, host removal and exploratory     │                                            │
-│                        │ analysis of samples.                      │                                            │
-│ ariba_characterization │                                           │                                            │
-│                mag_met │ 1- Bioinformatics best-practise analysis  │ https://github.com/nf-core/mag or          │
-│                        │ for taxonomic classification and          │ https://github.com/nf-core/taxprofiler     │
-│                        │ profiling; 2- Bioinformatics best-practise│                                            │
-│                        │ analysis pipeline for assembly, binning   │                                            │
-└────────────────────────┴───────────────────────────────────────────┴────────────────────────────────────────────┘
+┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
+┃        Service name ┃ Description                                                                                                              ┃ Github                                        ┃
+┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩
+│                IRMA │ Influenza fragment reconstruction and variant detection                                                                  │ https://github.com/CDCgov/irma                │
+│ assembly_annotation │ nf-core/bacass:  Simple bacterial assembly and annotation pipeline                                                       │ https://github.com/nf-core/bacass/tree/2.4.0  │
+│            blast_nt │ Alignment of de novo assembly contigs to database                                                                        │ -                                             │
+│    characterization │ Multi-Locus Sequence Typing (MLST), analysis of virulence factors, antimicrobial resistance and plasmid characterization │ -                                             │
+│             exomeeb │ Eukaria: Variant calling and annotation for a sequencing panel (e.g. epidermolysis gene panel, mouse or rat gene panel)  │ -                                             │
+│           exometrio │ Human: Exome sequencing for variant calling, annotation and inheritance filtering                                        │ -                                             │
+│  freebayes_outbreak │ Variant calling, annotation and SNP-based outbreak analysis (e.g. diploid fungal outbreak)                               │ -                                             │
+│       lowfreq_panel │ Low frequency variant calling from enrichment panel                                                                      │ -                                             │
+│           pikavirus │ PikaVirus, a mapping-based tool for metagenome analysis of virus                                                         │ https://github.com/BU-ISCIII/PikaVirus        │
+│  plasmidid_assembly │ Plasmid identification tool based on mapping and assisted by assembly                                                    │ https://github.com/BU-ISCIII/plasmidID        │
+│              rnaseq │ RNA-Seq analysis                                                                                                         │ https://github.com/nf-core/rnaseq             │
+│    seek_and_destroy │ Simple pipeline for basic quality control, host removal and exploratory analysis of samples                              │ https://github.com/GuilleGorines/Seek-Destroy │
+│              snippy │ Rapid haploid variant calling and core genome alignment                                                                  │ https://github.com/tseemann/snippy            │
+│         taxprofiler │ Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data                           │ https://github.com/nf-core/taxprofiler        │
+│          tbprofiler │ Mycobacterium tuberculosis variant calling and resistance prediction using TBProfiler                                    │ https://github.com/jodyphelan/TBProfiler      │
+│          viralrecon │ Viral genome reconstruction analysis for SARS-COV-2 data                                                                 │ https://github.com/BU-ISCIII/viralrecon       │
+│    wgmlst_chewbbaca │ Multilocus sequence typing (MLST) using chewBBACA                                                                        │ https://github.com/B-UMMI/chewBBACA           │
+│      wgmlst_taranis │ Multilocus sequence typing (MLST) using Taranis                                                                          │ https://github.com/BU-ISCIII/taranis          │
+│             wgstrio │ Human: Whole genome sequencing for SNPs variant calling, annotation and inheritance filtering                            │ -                                             │
+└─────────────────────┴──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┴───────────────────────────────────────────────┘
 ```
 
 #### new-service
 
 Example of usage:
 
 ```bash
-bu-isciii new-service <resolution_id>
+buisciii new-service <resolution_id>
 ```
 
 Help:
 
 ```bash
-Usage: bu-isciii new-service [OPTIONS] <resolution id>
+Usage: buisciii new-service [OPTIONS] <resolution id>
 
   Create new service, it will create folder and copy template depending on
   selected service.
@@ -186,13 +176,13 @@ Options:
 Example of usage:
 
 ```bash
-bu-isciii scratch --direction service_to_scratch <resolution_id>
+buisciii scratch --direction service_to_scratch <resolution_id>
 ```
 
 Help:
 
 ```bash
-Usage: bu-isciii scratch [OPTIONS] <resolution id>
+Usage: buisciii scratch [OPTIONS] <resolution id>
 
   Copy service folder to scratch directory for execution.
 
@@ -217,13 +207,13 @@ Options:
 Example of usage:
 
 ```bash
-bu-isciii finish <resolution_id>
+buisciii finish <resolution_id>
 ```
 
 Help:
 
 ```bash
-Usage: bu-isciii finish [OPTIONS] <resolution id>
+Usage: buisciii finish [OPTIONS] <resolution id>
 
   Service cleaning, remove big files, rename folders before copy and copy
   resolution FOLDER to sftp.
@@ -246,13 +236,13 @@ Finish module performs de following modules at onin this order, at once:
 Example of usage:
 
 ```bash
-bu-isciii clean <resolution_id>
+buisciii clean <resolution_id>
 ```
 
 Help:
 
 ```bash
-Usage: bu-isciii clean [OPTIONS] <resolution id>
+Usage: buisciii clean [OPTIONS] <resolution id>
 
   Service cleaning. It will either remove big files, rename folders before
   copy, revert this renaming, show removable files or show folders for no
@@ -278,21 +268,21 @@ Options:
 ##### scratch back
 
 ```bash
-bu-isciii scratch --direction scratch_to_service <resolution_id>
+buisciii scratch --direction scratch_to_service <resolution_id>
 ```
 
 ##### copy_sftp
 
 Example of usage:
 
 ```bash
-bu-isciii copy-sftp <resolution_id>
+buisciii copy-sftp <resolution_id>
 ```
 
 Help:
 
 ```bash
-Usage: bu-isciii copy-sftp [OPTIONS] <resolution id>
+Usage: buisciii copy-sftp [OPTIONS] <resolution id>
 
   Copy resolution FOLDER to sftp, change status of resolution in iskylims and
   generate md, pdf, html.
@@ -311,13 +301,13 @@ Options:
 Example of usage:
 
 ```bash
-bu-isciii bioinfo-doc <resolution_id>
+buisciii bioinfo-doc <resolution_id>
 ```
 
 Help:
 
 ```bash
-Usage: bu-isciii bioinfo-doc [OPTIONS] <resolution id>
+Usage: buisciii bioinfo-doc [OPTIONS] <resolution id>
 
   Create the folder documentation structure in bioinfo_doc server
 
@@ -342,13 +332,13 @@ Options:
 Example of usage:
 
 ```bash
-bu-isciii archive --date_from 2022-01-01 --date_until 2023-01-01
+buisciii archive --date_from 2022-01-01 --date_until 2023-01-01
 ```
 
 Help:
 
 ```bash
-Usage: bu-isciii archive [OPTIONS]
+Usage: buisciii archive [OPTIONS]
 
   Archive services or retrieve services from archive
 
@@ -375,13 +365,13 @@ Options:
 Example of usage:
 
 ```bash
-bu-isciii autoclean-sftp
+buisciii autoclean-sftp
 ```
 
 Help:
 
 ```bash
-Usage: bu-isciii autoclean-sftp [OPTIONS]
+Usage: buisciii autoclean-sftp [OPTIONS]
 
   Clean old sftp services
 
@@ -397,13 +387,13 @@ Options:
 Example of usage:
 
 ```bash
-bu-isciii fix-permissions -d /data/bi
+buisciii fix-permissions -d /data/bi
 ```
 
 Help:
 
 ```bash
-Usage: bu-isciii fix-permissions [OPTIONS]
+Usage: buisciii fix-permissions [OPTIONS]
 
   Fix permissions
 

buisciii/__init__.py

@@ -1,7 +1,6 @@
 #!/usr/bin/env python
-""" Main buisciii package file.
-"""
+"""Main BU-ISCIII package file"""
 
-import pkg_resources
+from importlib.metadata import version
 
-__version__ = pkg_resources.get_distribution("buisciii-tools").version
+__version__ = version("buisciii-tools")