beiko-lab/ARETE pipeline parameters
AMR/VF LGT-focused bacterial genomics workflow
Define where the pipeline should find input data and save output data.
| Parameter |
Description |
Type |
Default |
input_sample_table |
Path to comma-separated file containing information about the samples in the experiment. HelpYou will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. |
string |
|
outdir |
Path to the output directory where the results will be saved. |
string |
./results |
db_cache |
Directory where the databases are located |
string |
|
email |
Email address for completion summary. HelpSet this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (~/.nextflow/config) then you don't need to specify this on the command line for every run. |
string |
|
multiqc_title |
MultiQC report title. Printed as page header, used for filename if not otherwise specified. |
string |
|
Reference genome options
Reference and outgroup genome fasta files required for the workflow.
| Parameter |
Description |
Type |
Default |
reference_genome |
Path to FASTA reference genome file. |
string |
|
QC
| Parameter |
Description |
Type |
Default |
run_checkm |
Run CheckM QC software |
boolean |
|
apply_filtering |
Filter assemblies on QC results |
boolean |
|
skip_kraken |
Don't run Kraken2 taxonomic classification |
boolean |
|
min_n50 |
Minimum N50 for filtering |
integer |
10000 |
min_contigs_1000_bp |
Minimum number of contigs with >1000bp |
integer |
1 |
min_contig_length |
Minimum average contig length |
integer |
1 |
Annotation
Parameters for the annotation subworkflow
| Parameter |
Description |
Type |
Default |
annotation_tools |
Comma-separated list of annotation tools to run |
string |
mobsuite,rgi,cazy,vfdb,iceberg,bacmet,islandpath,phispy,report |
bakta_db |
Path to the BAKTA database |
string |
|
use_prokka |
Use Prokka (not Bakta) for annotating assemblies |
boolean |
|
min_pident |
Minimum match identity percentage for filtering |
integer |
60 |
min_qcover |
Minimum coverage of each match for filtering |
number |
0.6 |
skip_profile_creation |
Skip annotation feature profile creation |
boolean |
|
feature_profile_columns |
Columns to include in the feature profile |
string |
mobsuite,rgi,cazy,vfdb,iceberg,bacmet |
upset_plot_columns |
Columns to use for making Upset plots of genome features |
string |
|
Phylogenomics
Parameters for the phylogenomics subworkflow
| Parameter |
Description |
Type |
Default |
skip_phylo |
Skip Pangenomics and Phylogenomics subworkflow |
boolean |
|
use_ppanggolin |
Use ppanggolin for calculating the pangenome |
boolean |
|
use_full_alignment |
Use full alignment |
boolean |
|
use_fasttree |
Use FastTree |
boolean |
True |
feature_dispersion_columns |
Columns from the input samplesheet to use in the feature dispersion module |
string |
|
PopPUNK
Parameters for the lineage subworkflow
| Parameter |
Description |
Type |
Default |
skip_poppunk |
Skip PopPunk |
boolean |
|
poppunk_model |
Which PopPunk model to use (bgmm, dbscan, refine, threshold or lineage) |
string |
|
run_poppunk_qc |
Whether to run the QC step for PopPunk |
boolean |
|
enable_subsetting |
Enable subsetting workflow based on genome similarity |
boolean |
|
core_similarity |
Similarity threshold for core genomes |
number |
99.9 |
accessory_similarity |
Similarity threshold for accessory genes |
number |
99.0 |
Gene Order
Parameters for the Gene Order Subworkflow
| Parameter |
Description |
Type |
Default |
run_gene_order |
Whether to run the Gene Order subworkflow |
boolean |
|
input_file_path |
|
string |
/home/jvfe/dev/dalhousie/arete/test/gene-order/rgi_input.txt |
gene_order_percent_cutoff |
Cutoff percentage of genomes a gene should be present within to be included in extraction and subsequent analysis. Should a float between 0 and 1 (e.g., 0.25 means only genes present in a minimum of 25% of genomes are kept). |
number |
0.25 |
gene_order_label_cols |
If using annotation files predicting features, list of space separated column names to be added to the gene names |
string |
None |
num_neighbors |
Neighborhood size to extract. Should be an even number N, such that N/2 neighbors upstream and N/2 neighbors downstream will be analyzed. |
integer |
10 |
inflation |
Inflation hyperparameter value for Markov Clustering Algorithm. |
integer |
2 |
epsilon |
Epsilon hyperparameter value for DBSCAN clustering. |
number |
0.5 |
minpts |
Minpts hyperparameter value for DBSCAN clustering. |
integer |
5 |
plot_clustering |
Create Clustering HTML Plots |
boolean |
|
Recombination
Parameters for the recombination subworkflow
| Parameter |
Description |
Type |
Default |
run_recombination |
Run Recombination |
boolean |
|
run_verticall |
Run Verticall recombination tool |
boolean |
True |
run_gubbins |
Run Gubbins recombination tool |
boolean |
|
Dynamics
| Parameter |
Description |
Type |
Default |
run_evolccm |
Run the community coevolution model |
boolean |
|
run_rspr |
Run rSPR |
boolean |
|
min_rspr_distance |
Minimum rSPR distance used to define processing groups |
integer |
10 |
min_branch_length |
Minimum rSPR branch length |
integer |
0 |
max_support_threshold |
Maximum rSPR support threshold |
number |
0.7 |
max_approx_rspr |
Maximum approximate rSPR distance for filtering |
integer |
-1 |
min_heatmap_approx_rspr |
Minimum approximate rSPR distance used to generate heatmap |
integer |
0 |
max_heatmap_approx_rspr |
Maximum approximate rSPR distance used to generate heatmap |
integer |
-1 |
min_heatmap_exact_rspr |
Minimum exact rSPR distance used to generate heatmap |
integer |
0 |
max_heatmap_exact_rspr |
Maximum exact rSPR distance used to generate heatmap |
integer |
-1 |
core_gene_tree |
Core (or reference) genome tree. Used in the rSPR and evolCCM entries. |
string |
|
concatenated_annotation |
TSV table of annotations for all genomes. Such as the ones generated by Bakta or Prokka in ARETE. |
string |
|
feature_profile |
Feature profile TSV (A presence-absence matrix). Used in the evolCCM entry. |
string |
|
Institutional config options
Parameters used to describe centralised config profiles. These should not be edited.
| Parameter |
Description |
Type |
Default |
custom_config_version |
Git commit id for Institutional configs. |
string |
master |
custom_config_base |
Base directory for Institutional configs. HelpIf you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter. |
string |
https://raw.githubusercontent.com/nf-core/configs/master |
hostnames |
Institutional configs hostname. |
string |
|
config_profile_name |
Institutional config name. |
string |
|
config_profile_description |
Institutional config description. |
string |
|
config_profile_contact |
Institutional config contact information. |
string |
|
config_profile_url |
Institutional config URL link. |
string |
|
Max job request options
Set the top limit for requested resources for any single job.
| Parameter |
Description |
Type |
Default |
max_cpus |
Maximum number of CPUs that can be requested for any single job. HelpUse to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1 |
integer |
72 |
max_memory |
Maximum amount of memory that can be requested for any single job. HelpUse to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. --max_memory '8.GB' |
string |
125.GB |
max_time |
Maximum amount of time that can be requested for any single job. HelpUse to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. --max_time '2.h' |
string |
168.h |
Generic options
Less common options for the pipeline, typically set in a config file.
| Parameter |
Description |
Type |
Default |
help |
Display help text. |
boolean |
|
publish_dir_mode |
Method used to save pipeline results to output directory. HelpThe Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details. |
string |
copy |
email_on_fail |
Email address for completion summary, only when pipeline fails. HelpAn email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully. |
string |
|
plaintext_email |
Send plain-text email instead of HTML. |
boolean |
|
max_multiqc_email_size |
File size limit when attaching MultiQC reports to summary emails. |
string |
25.MB |
monochrome_logs |
Do not use coloured log outputs. |
boolean |
|
multiqc_config |
Custom config file to supply to MultiQC. |
string |
|
tracedir |
Directory to keep pipeline Nextflow logs and reports. |
string |
${params.outdir}/pipeline_info |
validate_params |
Boolean whether to validate parameters against the schema at runtime |
boolean |
True |
show_hidden_params |
Show all params when using --help HelpBy default, parameters set as hidden in the schema are not shown on the command line when a user runs with --help. Specifying this option will tell the pipeline to show all parameters. |
boolean |
|
enable_conda |
Run this workflow with Conda. You can also use '-profile conda' instead of providing this parameter. |
boolean |
|
singularity_pull_docker_container |
Instead of directly downloading Singularity images for use with Singularity, force the workflow to pull and convert Docker containers instead. HelpThis may be useful for example if you are unable to directly pull Singularity containers to run the pipeline due to http/https proxy issues. |
boolean |
|
schema_ignore_params |
|
string |
genomes,modules |
multiqc_logo |
|
string |
|