ONT_Autocycler

Full workflow for complete autocycler denovo assembly of bacterial genomes.

Workflow I/O

Inputs

input {
    File input_reads
    Int num_subsamples = 4
    Int min_read_depth_ss = 25
    Array[String] assemblers = ["raven", "miniasm", "flye", "metamdbg", "necat", "nextdenovo", "plassembler", "canu"]
    String read_type = "ont_r10"
    Int min_depth_abs = 5
    Float min_depth_rel = 0.1
    String? genomesize
    Int? max_contigs
    Int? kmer_size
    Float? cutoff
    Float? min_identity
    Int? max_unitigs
    Float? mad
}

Outputs

output {
    File atc_assemblies = FinalizeAssembly.assemblies
    File atc_autocycler_out = FinalizeAssembly.autocycler_out
    File atc_consensus_assembly_fa = FinalizeAssembly.consensus_assembly_fa
    File atc_consensus_assembly_gfa = FinalizeAssembly.consensus_assembly_gfa
    File atc_contig_headers = FinalizeAssembly.contig_headers
    Int atc_num_contigs = FinalizeAssembly.num_contigs
    File atc_final_log = ConsolidateLogs.final_log
}

---

Development

Dependencies

• uv
• make
• docker
• shellcheck

Setup dev environment

To get this all set up and groovy, simply ensure you have the dependencies listed above and execute ./dev_env/dev_setup.sh

Which does the following:

1. creates a virtual environment using uv
2. installs dev_deps.txt using uv. contents:
   • pre-commit to check files using the following linters at time before commit.
   • miniwdl for linting and checking wdl files. (needs shellcheck)
   • yamllint for linting and checking yaml files.
3. installs pre-commit to this repository.

Activate the virtual environment and you're good to go.

protip: I have these handy aliases in my .bashrc:

• alias uva="source .venv/bin/activate"
• alias uvd="deactivate"
• alias uvi="uv pip install"

Managing Tags and Versions

for versioning this workflow, be sure to change your version in .VERSION and use make tag to create and push the tag.

Manage versions for your containers in their respective makefiles.

Running miniwdl check without committing changes

just use make check and both miniwdl and yamllint will run on every *.wdl and *.yaml file in the project.