relecov-tools is a set of helper tools for the assembly of the different elements in the RELECOV platform (Spanish Network for genomic surveillance of SARS-Cov-2) as data download, processing, validation and upload to public databases, as well as analysis runs and database storage.
These tools require
- Python > 3.8
- 7-Zip (via the
p7zippackage) to handle compressed files. Please make sure it is installed before running the code.
On Debian/Ubuntu-based systems:
sudo apt update
sudo apt install p7zip-fullOn Red Hat/Fedora-based systems:
sudo dnf install p7zip p7zip-pluginsNote: For other distributions, please use your distribution's package manager to install
p7zip.
relecov-tools is available in Bioconda and can be installed via conda.
If you already have conda installed. Do the following:
conda config --add channels bioconda
conda create --name relecov-tools
conda activate relecov-tools
conda install -c bioconda relecov-toolsrelecov-tools is available in Pypi and can be installed via pip:
pip install relecov-toolsIf you want to install the latest code in the repository:
conda create -n relecov_dev pip
pip install --force-reinstall --upgrade git+https://github.com/bu-isciii/relecov-tools.git@develop
relecov-tools provides a command-line version with help descriptions and params prompt if needed.
$ relecov-tools --help
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RELECOV-tools version 1.6.0
Usage: relecov-tools [OPTIONS] COMMAND [ARGS]...
Options:
--version Show the version and exit.
-v, --verbose Print verbose output to the console.
-l, --log-path TEXT Creates log file in given folder. Uses default path in
config or tmp if empty.
-d, --debug Show the full traceback on error for debugging
purposes.
-h, --hex-code TEXT Define hexadecimal code. This might overwrite existing
files with the same hex-code
--help Show this message and exit.
Commands:
download Download files located in sftp server.
read-lab-metadata Create the json compliant to the relecov schema...
send-mail Send a sample validation report by mail.
validate Validate json file against schema.
map Convert data between phage plus schema to ENA,...
upload-to-ena parse data to create xml files to upload to ena
upload-to-gisaid parsed data to create files to upload to gisaid
update-db upload the information included in json file to...
read-bioinfo-metadata Create the json compliant from the Bioinfo...
metadata-homogeneizer Parse institution metadata lab to the one used...
pipeline-manager Create the symbolic links for the samples which...
build-schema Generates and updates JSON Schema files from...
logs-to-excel Creates a merged xlsx and Json report from all...
wrapper Executes the modules in config file sequentially
upload-results Upload batch results to sftp server.
add-extra-config Save given file content as additional configuration
Further explanation for each argument:
--verbose: Prints all logs as standard output, showing them to the user.--log-path: Use it to indicate a custom path for all logs to be saved. See Logging functionality for more information.--debug: Activate DEBUG logs. When not provided, logs will only show the most relevant information.--hex-code: By default all files generated will include a date and an unique hexadecimal code which is randomly generated upon execution. Using this argument you can pre-define the resulting hexadecimal code. NOTE: Keep in mind that this could overwrite existing files.
The command download connects to a transfer protocol (currently sftp) and downloads all files in the different available folders in the passed credentials. In addition, it checks if the files in the current folder match the files in the metadata file and also checks if there are md5sum for each file. Else, it creates one before storing in the final repository.
$ relecov-tools download --help
Usage: relecov-tools download [OPTIONS]
Download files located in sftp server.
Options:
-u, --user TEXT User name for login to sftp server
-p, --password TEXT password for the user to login
-f, --conf_file TEXT Configuration file (not params file)
-d, --download_option TEXT Select the download option: [download_only,download_clean, delete_only].
download_only will only download the files.
download_clean will remove files from sftp after download.
delete_only will only delete the files.
-o, --output_dir, TEXT Directory where the generated output will be saved
-t, --target_folders TEXT Flag: Select which folders will be targeted
giving [paths] or via prompt. For multiple
folders use ["folder1", "folder2"]
-s, --subfolder TEXT Flag: Specify which subfolder to process
(default: RELECOV)
--help Show this message and exit.
Configuration can be passed in several formats:
- if no config_file is passed, default values are fetched from conf/configuration.json, and user and password are asked in prompt.
- Default values can be overwritten using a yml config file, so you can input user, password, sftp_server, etc.
Config file example with all available options:
sftp_server: "sftprelecov.isciii.es"
sftp_port: "22"
sftp_user : "user"
sftp_passwd : "pass"
storage_local_folder: "/tmp/relecov"
tmp_folder_for_metadata: "/tmp/relecov/tmp"
allowed_sample_extensions:
- .fastq.gz
- .fasta
read-lab-metadata command reads the excel file with laboratory metadata and processes it adding additional needed fields.
$ relecov-tools read-lab-metadata --help
Usage: relecov-tools read-lab-metadata [OPTIONS]
Create the json compliant to the relecov schema from the Metadata file.
Options:
-m, --metadata_file PATH file containing metadata
-s, --sample_list_file PATH Json with the additional metadata to add to the received user metadata
-o, --output_dir, TEXT Directory where the generated output will be saved
-f, --files_folder PATH Path to folder where samples files are located
--help Show this message and exit.
An example for the metadata excel file can be found here
send-mail sends a validation summary report by email using predefined Jinja templates. It supports attachments, multiple recipients, and includes the option to add additional notes manually or via a .txt file.
$ relecov-tools send-email --help
Usage: relecov-tools send-email [OPTIONS]
Send a sample validation report by mail.
Options:
-v, --validate_file PATH Path to the validation summary json file
(validate_log_summary.json) [required]
-r, --receiver_email TEXT Recipient's e-mail address (optional). If not
provided, it will be extracted from the
institutions guide.
-a, --attachments PATH Path to file
-t, --template_path PATH Path to relecov-tools templates folder
(optional)
-p, --email_psswd TEXT Password for [email protected]
-n, --additional_notes PATH Path to a .txt file with additional notes to
include in the email (optional).
--help Show this message and exit.
read-bioinfo-metadata Include the results from the Bioinformatics analysis into the Json previously created with read-lab-metadata module.
$ relecov-tools read-bioinfo-metadata --help
Usage: relecov-tools read-bioinfo-metadata [OPTIONS]
Create the json compliant from the Bioinfo Metadata.
Options:
-j, --json_file PATH json file containing lab metadata
-s, --json_schema_file TEXT Path to the JSON Schema file used for
validation
-i, --input_folder PATH Path to input files
-o, --output_dir, --output-dir, --output_folder, --out-folder, --output_location, --output_path, --out_dir, --output DIRECTORY
Directory where the generated output will be
saved
-p, --software_name TEXT Name of the software/pipeline used.
--update If the output file already exists, ask if
you want to update it.
--soft_validation If the module should continue even if any
sample does not validate.
--help Show this message and exit.- Note: Software-specific configurations are available in bioinfo_config.json.
The bioinfo_config.json file is a configuration file used by the read-bioinfo-metadata module. Its purpose is to specify which files to search for and how to extract relevant information from a folder containing bioinformatics results. With this configuration, the module identifies parameters and results for each sample and returns them in a standardized JSON format.
Structure:
- Top Level: Bioinformatics Software Name
The top-level keys represent the name of the bioinformatics software used in the analysis (e.g.,"viralrecon"). Each block contains the configuration for extracting data generated by that specific pipeline.
- Second Level: Analysis Stages or Result Files
Within each software block, the keys correspond to different analysis stages or result files. Each section defines how to locate and process specific output files.
- Key Fields Explained
| Key | Description | Value Type |
|---|---|---|
fn |
Regular expression pattern to locate the corresponding files. | String (regex) |
sample_col_idx |
Index of the column containing the sample identifier (0-based). | Integer |
header_row_idx |
Index of the row containing the file header. | Integer |
required |
Indicates if the file is mandatory (true) or optional (false). |
Boolean |
function |
Name of a custom processing function (if applicable). Functions should be located in assets/pipeline_utils. |
String or null |
multiple_samples |
Specifies if the file contains data for multiple samples. | Boolean |
split_by_batch |
Indicates whether data should be separated by batches. | Boolean |
map |
Indicates whether the file's values should be mapped into the final metadata (j_data). If set to false, the file is still processed (e.g., to generate the long_table), but its content will not be included in j_data. |
Boolean |
extract |
If true, instructs the module to extract data from the file’s content. |
Boolean |
content |
Dictionary mapping standardized parameter names to the corresponding columns in the source file. | Object |
validate commands validate the data in json format outputted by read-metadata command against a json schema, in this case the relecov schema specification. It also creates a summary of the errors and warnings found in excel format as a report to the users.
$ relecov-tools validate --help
Usage: relecov-tools validate [OPTIONS]
Validate json file against schema.
Options:
-j, --json_file TEXT Json file to validate
-s, --json_schema_file TEXT Path to the JSON Schema file used for validation
-m, --metadata PATH Origin file containing metadata
-o, --output_dir, Directory where the generated output will be saved.
-e, --excel_sheet TEXT Optional: Name of the sheet in excel file to validate.
-r, --registry TEXT Path to registry (JSON file) with validated samples and their unique IDs.
--upload_files Wether to upload the resulting files from validation process or not.
-l, --logsum_file TEXT Required if --upload_files. Path to the log_summary.json file merged from all
previous processes, used to check for invalid samples.
--help Show this message and exit.
The command map converts a data in json format from relecov data model to ena or gisaid data model using their own schemas acording to their annotated ontology terms.
$ relecov-tools map --help
Usage: relecov-tools map [OPTIONS]
Convert data between phage plus schema to ENA, GISAID, or any other schema
Options:
-p, --origin_schema TEXT File with the origin (relecov) schema
-j, --json_file TEXT File with the json data to convert
-d, --destination_schema [ENA|GISAID|other]
schema to be mapped
-f, --schema_file TEXT file with the custom schema
-o, --output_dir, Directory where the generated output will be saved.
--help Show this message and exit.
upload-to-ena command uses json data mapped to ena schema to use the ena_upload_cli package to upload raw data and metadata to ENA db.
Usage: relecov-tools upload-to-ena [OPTIONS]
parsed data to create xml files to upload to ena
Options:
-u, --user user name for login to ena
-p, --password password for the user to login
-c, --center center name
-e, --ena_json where the validated json is
-t, --template_path path to folder containing ENA xml templates
-a, --action select one of the available options: [add|modify|cancel|release]
--dev Flag: Test submission
--upload_fastq Flag: Upload fastq files. Mandatory for "add" action
-m", --metadata_types List of metadata xml types to submit [study,experiment,run,sample]
-o, --output_dir Directory where the generated output will be saved.
--help Show this message and exit.
upload-to-gisaid uses the json mapped to gisaid schema to upload raw data and metadata to GISAID db
Usage: relecov-tools upload-to-gisaid [OPTIONS]
parsed data to create xml files to upload to ena
Options:
-u, --user TEXT user name for login
-p, --password TEXT password for the user to login
-c, --client_id TEXT client-ID provided by [email protected]
-t, --token TEXT path to athentication token
-e, --gisaid_json TEXT path to validated json mapped to GISAID
-i, --input_path TEXT path to fastas folder or multifasta file
-o, --output_dir, Directory where the generated output will be saved.
-f, --frameshift [catch_all|catch_none|catch_novel]
frameshift notification
-x, --proxy_config TEXT introduce your proxy credentials as:
username:password@proxy:port
--single input is a folder with several fasta files.
Default: False
--gzip input fasta is gziped. Default: False
--help Show this message and exit.
Upload the information included in json file to the database
Usage: relecov-tools update-db [OPTIONS]
upload the information included in json file to the database
Options:
-j, --json TEXT data in json format
-t, --type [sample|bioinfodata|variantdata]
Select the type of information to upload to
database
-plat, --platform [iskylims|relecov]
name of the platform where data is uploaded
-u, --user TEXT user name for login
-p, --password TEXT password for the user to login
-s, --server_url TEXT url of the platform server
-f, --full_update Sequentially run every update option
-l, --long_table TEXT Long_table.json file from read-bioinfo-
metadata + viralrecon
--help Show this message and exit.
Create the folder structure to execute the given pipeline for the latest sample batches after executing download, read-lab-metadata and validate modules. This module will create symbolic links for each sample and generate the necessary files for pipeline execution using the information from validated_BATCH-NAME_DATE.json.
Usage: relecov-tools pipeline-manager [OPTIONS]
Create the symbolic links for the samples which are validated to prepare for
bioinformatics pipeline execution.
Options:
-i, --input PATH select input folder where are located the sample
files
-t, --templates_root PATH Path to folder containing the pipeline templates
from buisciii-tools
-c, --config PATH select the template config file
-o, --output_dir, Directory where the generated output will be saved.
-f, --folder_names TEXT Folder basenames to process. Target folders names
should match the given dates. E.g. ... -f folder1
-f folder2 -f folder3
--help Show this message and exit.
Execute download, read-lab-metadata and validate sequentially using a config file to fill the arguments for each one. It also creates a global report with all the logs for the three processes in a user-friendly .xlsx format. The config file should include the name of each module that is executed, along with the necessary parameters in YAML format.
Usage: relecov-tools wrapper [OPTIONS]
Executes the modules in config file sequentially
Options:
-c, --config_file PATH Path to config file in yaml format [required]
-o, --output_dir, Directory where the generated output will be saved [required].
--help Show this message and exit.
Creates an xlsx file with all the entries found for a specified laboratory in a given set of log_summary.json files (from log-summary module). The laboratory name must match the name of one of the keys in the provided logs to work.
Usage: relecov-tools logs-to-excel [OPTIONS]
Creates a merged xlsx report from all the log summary jsons given as input
Options:
-l, --lab_name Name for target laboratory in log-summary.json files
-o, --output_dir, Directory where the generated output will be saved [required].
-f, --files Paths to log_summary.json files to merge into xlsx file, called once per file
This command is used to create an additional config file that will override the configuration in conf/configuration.json. You may pass this configuration in a YAML or JSON file. If you want the keys in your additional configuration to be grouped under a certain keyname, use param -n, --config_name. Otherwise, the file content will be parsed with no additional processing.
Usage: relecov-tools add-extra-config [OPTIONS]
Save given file content as additional configuration
Options:
-n, --config_name TEXT Name of the config key that will be added
-f, --config_file TEXT Path to the input file: Json or Yaml format
--force Force replacement of existing configuration if
needed
--clear_config Remove given config_name from extra config: Use with
empty --config_name to remove all
--help Show this message and exit.
The build-schema module provides functionality to generate and manage JSON Schema files based on database definitions from Excel spreadsheets. It automates the creation of JSON Schemas, including validation, drafting, and comparison with existing schemas. Uses the generated JSON schema to create a structured Excel template.
Usage: relecov-tools build-schema [OPTIONS]
Generates and updates JSON Schema files from Excel-based database
definitions.
Options:
-i, --input_file PATH Path to the Excel document containing the
database definition. This file must have a
.xlsx extension. [required]
-s, --schema_base PATH Path to the base schema file. This file is
used as a reference to compare it with the
schema generated using this module.
(Default: installed schema in 'relecov-tools
/relecov_tools/schema/relecov_schema.json')
-e, --excel_template PATH Path to the excel template file. This file
is used to get version history of the excel
template (stored in assets/Relecov_metadata_*.xlsx)
-v, --draft_version TEXT Version of the JSON schema specification to
be used. Example: '2020-12'. See:
https://json-schema.org/specification-links
-d, --diff Prints a changelog/diff between the base and
incoming versions of the schema.
--version TEXT Specify the schema version.
-p, --project TEXT Specficy the project to build the metadata
template.
--non-interactive Run the script without user interaction,
using default values.
-o, --output_dir, --output-dir, --output_folder, --out-folder, --output_location, --output_path, --out_dir, --output DIRECTORY
Directory where the generated output will be saved
--help Show this message and exit.
Ensure that the fields below are properly defined as headers in your Excel sheet (database definition):
enum: List of possible values for enumeration.
examples: Example values for the property.
ontology_id: Identifier for ontology.
type: Data type of the property (e.g., string, integer).
description: Description of the property.
classification: Classification or category of the property.
label_name: Label or name for the property.
fill_mode: Mode for filling in the property (e.g., required, optional).
required (Y/N): Indicates if the property is required (Y) or optional (N).
complex_field (Y/N): Indicates if the property is a complex (nested) field (Y) or a standard field (N).relecov-tools generate logs by default for all processes using a standard name: <module>_<batch-date>_<hexcode>.log
The --log-path given via command-line interface (CLI) is used to specify the destination directory where logs will be saved during execution When provided, it overrides the default logging behavior and directs all log files to the specified folder.
How default Logs are generated (when --log-path is not used):
Use a predefined default location found in configuration.json under logs_config key. If the module executed is found in
modules_outpath subkey, the log will be generated in the specified folder, otherwise it will be generated in default_outpath/module
If you want your logs to be sent to custom locations depending on the module executed you can do so by using add-extra-config, providing
After executing each of these modules, you may find a custom log report in json format named EXECUTED-MODULE_<date>_hex_log_summary.json. These custom log summaries can be useful to detect errors in metadata in order to fix them and/or notify the users.
relecov-tools is designed in a way that you can use import the different modules and use them in your own scripts, for example:
import relecov_tools.sftp_handle
user="admin"
passwd="1234"
conf_file="/path/to/conf"
sftp_connection = relecov_tools.sftp_handle.SftpHandle(
user, password, conf_file
)
sftp_connection.download()DOCs soon!!
Python package idea and design is really inspired in nf-core/tools.