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Running SQANTI3 from the wrapper

SQANTI3 v5.4: Simplified Execution with Wrapper Script and Configuration File

As of release v5.4, SQANTI3 introduces a streamlined way to run the pipeline using a unified wrapper script and a YAML configuration file. This update aims to simplify SQANTI3 execution by consolidating all parameters for a given run—from quality control (QC) through filtering and rescue—into a single, easily managed file.

To ensure a smooth experience with SQANTI3, follow these recommendations:

  • Add SQANTI3 to your PATH:
    Make the wrapper script accessible system-wide by either adding the SQANTI3 directory to your PATH or creating a symbolic link to the sqanti3 script in a directory already in your PATH.

  • Use a configuration file per experiment:
    Maintain one YAML configuration file per experiment. This allows you to tweak parameters directly from the command line for each run.

  • Version control your configuration files:
    Keep your configuration files under version control (e.g., git) to track parameter changes across different runs and experiments.

Adding SQANTI3 to the PATH in Ubuntu You can add the wrapper script to your PATH in two ways: - **Option 1: Add the SQANTI3 directory to your PATH** ```bash export PATH=$PATH:/path/to/SQANTI3 ``` Add this line to your `.bashrc` file to make it persistent across sessions. - **Option 2: Create a symbolic link** ```bash ln -s /path/to/SQANTI3/sqanti3 /usr/local/bin/sqanti3 ```


Configuration File

The configuration file is written in YAML (⚠️ must use the .yaml extension). It contains all arguments and parameters required by the SQANTI3 modules and flags to select which modules (qc, filter, rescue) to run. For the filter and rescue modules, you can specify whether to use rules-based or machine learning approaches.

Structure: - Common options: Shared across all modules (e.g., reference genome, maximum threads). - Module-specific options: Parameters unique to QC, filter, or rescue.

Creating a Configuration Template: Generate a template with default parameters using:

sqanti3 init -c sqanti3_config.yaml

If you omit the filename (sqanti3 init -c), it defaults to sqanti3_config.yaml.

Overriding Parameters: You can override configuration values directly from the command line using the -a flag:

sqanti3 init -c sqanti3_config.yaml -a cpus=8 dir=sqanti3_results

The -a flag can also be used when running SQANTI3 to temporarily override config values for a specific run.

View Available Arguments: Use the -h flag after a module name to list all available arguments and their default values.

Path Handling: Paths in the configuration file can be absolute or relative. Relative paths are resolved from the directory where you execute the sqanti3 command.

❓Example Configuration File 
main:
  refGTF: ''
  refFasta: ''
  cpus: 4
  dir: sqanti3_results
  output: isoforms
  log_level: INFO
qc:
  enabled: true
  options:
    isoforms: ''
    min_ref_len: 0
    force_id_ignore: false
    fasta: false
    genename: false
    novel_gene_prefix: ''
    sites: ATAC,GCAG,GTAG
    window: 20
    aligner_choice: minimap2
    gmap_index: ''
    include_ORF: false
    orf_input: ''
    psauron_threshold: 0.5
    short_reads: ''
    SR_bam: ''
    CAGE_peak: ''
    polyA_motif_list: ''
    polyA_peak: ''
    phyloP_bed: ''
    expression: ''
    coverage: ''
    fl_count: ''
    isoAnnotLite: false
    gff3: ''
    saturation: false
    report: html
    isoform_hits: false
    ratio_TSS_metric: max
    chunks: 1
    is_fusion: false
    tusco: ''
filter:
  enabled: true
  options:
    common:
      sqanti_class: sqanti3_results/isoforms_classification.txt
      isoAnnotGFF3: ''
      filter_isoforms: sqanti3_results/isoforms_corrected.fasta
      filter_gtf: sqanti3_results/isoforms_corrected.gtf
      filter_sam: ''
      filter_faa: ''
      skip_report: false
      filter_mono_exonic: false
    rules:
      enabled: true
      options:
        json_filter: <path_to>/SQANTI3/src/utilities/filter/filter_default.json
    ml:
      enabled: false
      options:
        percent_training: 0.8
        TP: ''
        TN: ''
        threshold: 0.7
        force_fsm_in: false
        intermediate_files: false
        remove_columns: ''
        max_class_size: 3000
        intrapriming: 60
rescue:
  enabled: true
  options:
    filter_class: sqanti3_results/isoforms_RulesFilter_result_classification.txt
    corrected_isoforms_fasta: sqanti3_results/isoforms_corrected.fasta
    filtered_isoforms_gtf: sqanti3_results/isoforms.filtered.gtf
    refClassif: ''
    counts: ''
    rescue_mono_exonic: all
    mode: automatic
    requant: false
    strategy: rules
    json_filter: <path_to>/SQANTI3/src/utilities/filter/filter_default.json
    random_forest: sqanti3_results/isoformsrandomforest.RData
    threshold: 0.7


Best Practices

  • Test your configuration with --dry-run:
    Before running the full pipeline, use the --dry-run flag to preview the commands that will be executed without actually running them. bash sqanti3 all -c sqanti3_config.yaml --dry-run

  • Get module-specific help:
    View detailed help for each module with: bash sqanti3 qc -h sqanti3 filter -h sqanti3 rescue -h

  • Keep configuration files organized:
    Use descriptive names for your config files (e.g., experiment1_config.yaml, sample_A_config.yaml) to easily identify different runs.

Running SQANTI3

After creating your configuration file, you can run SQANTI3 in two main ways:

  • Run all activated modules (QC, filter, rescue): bash sqanti3 all -c sqanti3_config.yaml

  • Run a specific module: bash sqanti3 qc -c sqanti3_config.yaml sqanti3 filter -c sqanti3_config.yaml sqanti3 rescue -c sqanti3_config.yaml

Override parameters for a single run:

sqanti3 qc -c sqanti3_config.yaml -a short_reads=/path/to/short_reads.fastq dir=/path/to/output

This command temporarily changes the short reads file and output directory for this run only.

❓Help message 
usage: sqanti3 {all,qc,filter,rescue,init} [-c CONFIG] [--dry-run] [-a ARGUMENTS [ARGUMENTS ...]] [-h] [-l {ERROR,WARNING,INFO,DEBUG}]

Python wrapper for SQANTI3 pipeline.

positional arguments:
  {all,qc,filter,rescue,init}  Action to perform

options:
  -c CONFIG, --config CONFIG   Path to the configuration file (default: sqanti3_config.yaml)
  --dry-run                    Print the commands that would be executed
  -a ARGUMENTS [ARGUMENTS ...], --arguments ARGUMENTS [ARGUMENTS ...]
                               Non-default arguments to pass to the SQANTI3 modules
  -h, --help                   Show the help message and exit
  -l {ERROR,WARNING,INFO,DEBUG}, --log_level {ERROR,WARNING,INFO,DEBUG}
                               Set the logging level (default: INFO)