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Karla Vasco edited this page Jun 26, 2026 · 3 revisions

⚙️ Pipeline Parameters

This page documents all parameters available for CorGe+.

Pipeline parameters use double hyphens (--), while Nextflow runtime options use single hyphens (-).

Example:

nextflow run MDHHS-Bioinformatics/corge \
  -profile apptainer \
  --input manifest.csv \
  --cgmlst_schemas cgmlst_schemas.csv \
  --outdir corge_results

📥 Core Pipeline Parameters

These parameters are required for most pipeline runs.

Parameter Type Required Default Description
--input string ✓ – Manifest CSV (sample,assembly,species).
--outdir string ✓ ./corge_results Output directory (acts as a growing database across runs).
--cgmlst_schemas string – – CSV mapping species to cgMLST schemas (species,cgmlst_path).
--hc_thresholds string ✓ 15,20,40,150 Hierarchical-clustering thresholds (method single) for grouping samples. They represent allelic or SNP distances depending on the analysis performed. Comma-separated (no spaces).
--mode string ✓ default Pipeline mode: default, download_schema, create_schema, regroup, remove or tree.
--tree boolean – false Build a maximum-likelihood phylogenetic tree (GTR+G4) from a DNA multiple-sequence alignment (MSA). By default, the pipeline outputs only distance-based trees (MashTree and MSTreeV2 from allele or SNP distances). Enabling this option requires substantially more computational time and resources. When a cgMLST schema is used, the MSA is derived from the cgMLST allelic profiles. Only when using modes default or remove
--use_previous_partitions_for_snp boolean ✓ false Force reuse of previous clustering nomenclature for SNP-based analysis done with Parsnp. Not recommended, it can take several hours to resolve.

🧬 Analysis Options

These parameters control analysis behavior.

Parameter Type Default Description
--schema_ids string – cgMLST schema IDs (required for --mode schema). Comma-separated (no spaces).
--samples_to_remove string – CSV of samples to remove (required for --mode remove, columns: sample,species).
--species string – Species to reanalyze using prior results from outdir (required for --mode regroup or --mode tree). Also required for --mode create_schema.
--assembly_sheet string – Text file with one assembly FASTA path per line. Required for --mode create_schema. Supports .fa, .fas, .fasta, .fna, and gzipped versions.
--reference_path string – Path to reference/representative assembly FASTA used to generate the Prodigal training file for --mode create_schema. Supports .fa, .fas, .fasta, .fna, and gzipped versions.
--cgmlst_threshold number 0.95 Core-genome threshold for defining the cgMLST schema in --mode create_schema. Must be a single value > 0 and <= 1.

📦 Read and annotation file source options (PoODLE)

Optional parameters to populate PoODLE manifests automatically.

Parameter Type Default Description
--master_paths string – CSV with explicit absolute paths to reads and annotations (sample,fastq_1,fastq_2,annotation). Use this when you already have all paths from the database organized in a single file.
--phoenix_path string – Path to PHoeNIx results directory.
--bactopia_path string – Path to Bactopia results directory.

⚠ Only one of these options should be used per run. If your data was priorly processed with PHoeNIx or Bactopia, CorGe+ will infer read and annotation paths based on sample IDs.

🌳 ReporTree Metadata Options

ReporTree can link genetic clusters with epidemiological data through summary tables showing key statistics and trends. These parameters are optional but strongly recommended when generating lineage-, time-, or metadata-based reports.

Parameter Type Default Description
--metadata string – Metadata table (CSV/TSV) used for reporting. Must include all samples (new + previous) for the species. Sample IDs in the first column must match CorGe+ names. Recommended to include a date column (YYYY-MM-DD) for temporal summaries.
--columns_summary_report string predefined set Metadata columns to summarize per cluster. Supports counts (n_country), distributions (country), and-if a date column exists-temporal measures (first/last sample date and time span). Useful for generating cluster-level epidemiological summaries. (default: n_sequence,lineage,n_country,country,n_region,first_seq_date,last_seq_date,timespan_days)
--metadata2report string – Additional metadata columns for which separate summary reports should be created. Useful when tracking specific fields (e.g.,st,source,serotype,AMR_profile).
--filter string – Filter samples before analysis using expressions such as 'country == USA' or 'country == USA;date > 2024-01-01'. Supports multiple conditions and multiple columns.
--frequency_matrix string – Generate frequency matrices showing the proportion of samples for variable combinations (e.g., 'lineage,iso_week' → lineage distribution over time). Supports multiple matrices.
--count_matrix string – Same as --frequency_matrix but outputs raw counts instead of percentages. Useful for plotting absolute numbers across time or categories.

More details about these options in ReporTree.

⚙️ Execution Configuration

These parameters control compute resource limits.

Parameter Type Default Description
--max_cpus integer 16 Maximum CPUs that can be requested by any job.
--max_memory string 128.GB Maximum memory that can be requested by any job.
--max_time string 24.h Maximum execution time for any job.

🔧 Generic Pipeline Options

These parameters control pipeline behavior.

Parameter Type Default Description
--help boolean – Display help message and exit.
--version boolean – Print pipeline version and exit.
--validate_params boolean true Validate parameters against schema.
--show_hidden_params boolean false Show advanced parameters in help output.
--monochrome_logs boolean false Disable colored logging output.

🧠 Core Nextflow Arguments

These options are part of Nextflow itself and use a single hyphen (-).

-profile

Select the execution configuration profile.

Example:

-profile singularity

Available profiles:

Profile Description
docker Run using Docker containers
apptainer Run using Apptainer containers
singularity Run using Singularity containers
test Run pipeline with bundled test data
test_full Run pipeline with bundled full test data

Multiple profiles can be combined:

-profile test,singularity

-r (Pipeline Release Version)

Specify the pipeline version or Git revision to run.

Example:

nextflow run MDHHS-Bioinformatics/corge -r v1.0.0

This ensures that the exact same pipeline version is used for analysis.

You can also run:

Example Description
-r v1.0.0 Run a tagged release
-r main Run the latest development version
-r <commit> Run a specific Git commit

⚠️ For reproducible analyses, it is strongly recommended to run a tagged release.

-resume

Resume a previously failed or interrupted pipeline run.

-resume

Nextflow will reuse cached results when possible.

-c

Provide a custom Nextflow configuration file.

-c custom.config

🏛 Institutional Configuration Options

These parameters are used when loading configurations from nf-core/configs.

Parameter Description
--custom_config_version Git commit ID for institutional configs
--custom_config_base Base URL for institutional configuration repository
--config_profile_name Name of institutional profile
--config_profile_description Description of institutional profile
--config_profile_contact Contact information
--config_profile_url Documentation URL

⚡ Custom Configuration (Advanced)

Users can override pipeline resource requirements using custom configuration files.

Example:

process {
    withName: ALIGNMENT {
        memory = 100.GB
        cpus = 8
    }
}

Run with:

nextflow run corge -c custom.config

🧰 Troubleshooting Resource Issues

If a job fails due to insufficient memory or CPUs, you can increase global resource limits:

--max_memory 200.GB \
--max_cpus 32 \
-resume

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