Workflow

Usage:

Usage:

nextflow run -c <custom config> -profile <profile> -params-file params.yml <nextflow script> [ -entry VALIDATE_SEQUENCES ]

where

There are two workflows which can be run.

• VALIDATE_SEQUENCES only: Enable by including -entry VALIDATE_SEQUENCES in the workflow run command. Runs only the sequence validation workflow.
• Full workflow: The full workflow is the default mode of running and runs both the VALIDATE_SEQUENCES workflow and SELECTION_ANALYSES workflow.

Workflow parameters should be supplied using a params.yml file.

params.yml:

# NAISS Compute allocation (only for -profile dardel)
project: 'naiss20XX-YY-ZZ'

# workflow parameters
gene_sequences: /path/to/gene/sequences/*.fasta
species_tree: /path/to/species.tree
species_labels: /path/to/species.tsv # Optional two column file of species and their labels
run_codonphyml: false

# Tool settings
hyphy_test:
    absrel:
        U-01: '--branches Leaves'
        L-02: '--branches CB' # 'L-' prefix denotes species labels should be used
    BUSTED-PH.bf:
        L-11: '--branches CB --comparison PB --srv No'

# output
results: './results'

Hyphy tests are supplied to workflow using a nested mapping. The top level key is the name of the test, and the key value pair underneath is the output label and settings to use. If the output label is prefixed with an L-, then the species labels are also supplied to Hyphy.

Override cpu, memory, and time resources by creating a nextflow.config in your launch directory (where you run nextflow run ...), that looks like:

process {
    withName: 'PRANK' {
        cpus   = 2
        memory = 20.GB
        time   = 1.d
    }
}

Workflow parameter inputs

Mandatory:

• gene_sequences: A set of gene sequences in fasta format to be sanitized and aligned.
• species_tree: A species tree in Newick format to guide alignment.
• hyphy_test: The hyphy branch-site test to use. See parameter file above to see how tests and settings are supplied.

Optional:

• species_labels: A two column file of species and their labels.
• run_codonphyml: If true, run codonphyml to make a gene tree for hyphy (default: false)
• results: The publishing path for results (default: results).
• publish_mode: (values: 'symlink', 'copy' (default)) The file publishing method from the intermediate results folders (see Table of publish modes).

Workflow outputs

All results are published to the path assigned to the workflow parameter results.

• 00_Problematic_Sequences: Sequences that failed sanitation. Intermediate stop codons were found.
• 01_Sanitized_Sequences/: Sanitized gene sequences with trailing stop codons removed.
• 02_Prank_alignment/: Phylogenetically guided gene sequence alignments.
• 03_Codonphyml/: Reconstructed phylogeny.
• 04_HyPhy_selection_analysis/<test>-<id>: Hyphy selection analyses, and TSV of results.
• pipeline_info/: A folder containing workflow execution details (if -profile pipeline_info).

Customisation for PDC-KTH

Custom profiles named dardel and dardel_local are available to run this workflow specifically on PDC-KTH clusters. The dardel profile utilizes the nf-core pdc-kth profile which enables using the slurm executor so jobs are submitted to the Slurm Queue Manager. All jobs submitted to slurm must be associated to a NAISS project which is supplied using the --project workflow parameter. All jobs are executed within Apptainer containers (formerly Singularity). Remember to use module load PDC apptainer in order to use Apptainer with the workflow. Similarly, the dardel_local profile also uses Singularity containers, but executes everything locally. Follow the instructions on PDC_KTH - Interactive running for running a job locally.

module load PDC apptainer
nextflow run -profile dardel main.nf

Project structure

The workflow in this folder manages the execution of your analyses from beginning to end.

Nextflow-selection-workflow/
 | - bin/                            Custom workflow scripts
 | - configs/                        Configuration files that govern workflow execution
 | - containers/                     Custom container definition files
 | - modules/                        Nextflow process definitions used in main.nf
 | - main.nf                         The workflow definition script
 \ - nextflow.config                 General Nextflow configuration