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rpetit3rpetit3
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add a test workflow
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‎.github/workflows/build.yml‎

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@@ -51,4 +51,4 @@ jobs:
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run: make install
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- name: Test
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run: nextflow run nf-bactopia-test/ -plugins nf-bactopia@0.1.0
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run: nextflow run nf-bactopia-test/ -plugins nf-bactopia@0.1.0 --help

‎README.md‎

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@@ -31,14 +31,18 @@ conda create -y -n nf-bactopia \
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conda activate nf-bactopia
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```
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### Build the plugin
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### Build the plugin and install
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```{bash}
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make assemble
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make install
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```
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### Use the plugin
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The `make install` should put the plugin in your `~/.nextflow/plugins` directory. So it should
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just work!
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```{bash}
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NXF_VER=25.06.0-edge NXF_PLUGINS_DIR=/path/to/build/plugins nextflow run ...
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NXF_VER=25.06.0-edge nextflow run ...
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```

‎nf-bactopia-test/conf/base.config‎

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process {
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// Defaults
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container = "bactopia/bactopia:${params.bactopia_version}"
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errorStrategy = 'retry'
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maxRetries = params.max_retry
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// Resource Limits
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resourceLimits = [
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cpus: params.max_cpus,
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memory: params.max_memory,
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time: params.max_time
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]
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// Resources
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cpus = { 1 * task.attempt }
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memory = { 4.GB * task.attempt }
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time = { 1.h * task.attempt }
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// Modules imported from nf-core
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withLabel: process_single {
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cpus = { 1 }
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memory = { 4.GB * task.attempt }
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time = { 2.h * task.attempt }
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}
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withLabel: process_low {
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cpus = { 4 * task.attempt }
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memory = { 8.GB * task.attempt }
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time = { 4.h * task.attempt }
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}
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withLabel: process_medium {
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cpus = { 8 * task.attempt }
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memory = { 32.GB * task.attempt }
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time = { 12.h * task.attempt }
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}
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withLabel: process_high {
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cpus = { 12 * task.attempt }
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memory = { 64.GB * task.attempt }
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time = { 24.h * task.attempt }
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}
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withLabel: process_long {
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time = { 96.h * task.attempt }
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}
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withLabel: process_high_memory {
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memory = { 128.GB * task.attempt }
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}
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withLabel: error_ignore {
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errorStrategy = 'ignore'
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}
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withLabel: error_retry {
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errorStrategy = 'retry'
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maxRetries = 2
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}
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}

‎nf-bactopia-test/conf/outputs.config‎

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// Used to set the output directory of modules
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params {
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publish_dir {
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annotate_genome = "annotation"
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antimicrobial_resistance = "antimicrobial-resistance"
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assemble_genome = "assembly"
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assembly_qc = "assembly"
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blast = "blast"
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call_variants = "variants"
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count_31mers = "minmers"
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mapping_query = "mapping"
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minmer_query = "minmers"
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minmer_sketch = "minmers"
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qc_reads = "quality-control"
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sequence_type = "mlst"
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// These produce *-error.txt that should go to the root
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gather_samples = ""
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}
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}

‎nf-bactopia-test/conf/params.config‎

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/*
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This file includes default values for shared parameters.
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*/
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params {
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wf = "bactopia"
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list_wfs = false
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bactopia = null
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outdir = params.bactopia ? params.bactopia : "bactopia"
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run_name = "${params.wf}"
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rundir = null
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skip_compression = false
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keep_all_files = false
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merge_folder = "merged-results"
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//nf-core
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schema_ignore_params = 'rundir,mix_downloads,no_check_certificate,run_name,prokka_debug,is_ci,sourmash_url,mash_url,mlst_url,amrfinder_url,merge_folder,wf_has_subdir,build_all,use_mamba,empty_proteins,empty_tf,empty_adapters,empty_phix,help_all,include_tools,publish_dir,silent,test_data,test_data_dir,verbose,schema_inputs,empty_extra,empty_r2,empty_r1,workflows,available_workflows,is_subworkflow,enable_conda,force_rebuild,config_profile_url,config_profile_contact,config_profile_description,config_profile_name'
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schema_inputs = ['fastqs', 'r1,r2,se,sample,hybrid', 'r1,r2,sample', 'se,sample', 'assembly,sample', 'accessions', 'accession']
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// Max Job Request Parameters
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max_retry = 3
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max_time = 240.h
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max_memory = 128.GB
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max_cpus = 4
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max_downloads = 3
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// Nextflow Configuration Parameters
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/* Nextflow config files
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nfconfig - allows you to provide your own config file to Nextflow
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What this means is you can adjust process rules such as max runtimes, cpu and
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memory usage, etc...
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Most importantly, this means you can create a profile that allows you to better
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use Bactopia in your environment. This will allow you to create a profile
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for things such as Sun Grid Engine, SLURM, AWS, etc...
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If you provide a config, its loaded after the default configs. So any changes
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to the defaults in your config will be reflected.
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Links to Nextflow Docs:
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Nextflow Docs: https://www.nextflow.io/docs/latest/config.html#scope-process
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Nextflow Docs: https://www.nextflow.io/docs/latest/config.html#config-profiles
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Nextflow Executors: https://www.nextflow.io/docs/latest/executor.html
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*/
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nfconfig = null
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publish_dir_mode = 'copy'
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force = false
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cleanup_workdir = false
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// Nextflow Profile Parameters
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condadir = "${params.bactopia_cache}/conda"
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singularity_cache = "${params.bactopia_cache}/singularity"
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singularity_pull_docker_container = false
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force_rebuild = false
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container_opts = ""
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registry = "quay.io"
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// Generic Parameters
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help = null
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help_all = false
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sleep_time = 5
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validate_params = true
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//nf-core
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monochrome_logs = false
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enable_conda = false
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show_hidden_params = false
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// Parameters to ignore
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build_all = false
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include_tools = null
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verbose = null
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silent = null
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no_check_certificate = false
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// Datasets Parameters
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datasets_cache = "${params.bactopia_cache}/datasets"
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amrfinder_url = "https://datasets.bactopia.com/datasets/v${params.bactopia_version}/amrfinderplus.tar.gz"
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mlst_url = "https://datasets.bactopia.com/datasets/v${params.bactopia_version}/mlst.tar.gz"
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mash_url = "https://datasets.bactopia.com/datasets/mash-refseq88.k21.msh.xz"
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sourmash_url = "https://datasets.bactopia.com/datasets/gtdb-rs207.genomic-reps.dna.k31.lca.json.gz"
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// Testing
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test_data_dir = 'https://raw.githubusercontent.com/bactopia/bactopia-tests/main/data'
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is_ci = false
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// Config options
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config_profile_name = null
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config_profile_description = null
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custom_config_version = 'master'
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custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
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config_profile_contact = null
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config_profile_url = null
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}

‎nf-bactopia-test/conf/params/bactopia-tools.config‎

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/*
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This file includes default values for shared parameters.
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*/
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params {
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is_subworkflow = true
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// Bactopia Tools
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include = null
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exclude = null
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// Mix downloads with local samples
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mix_downloads = true
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}

‎nf-bactopia-test/conf/profiles.config‎

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profiles {
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standard {
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conda.enabled = true
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conda.cacheDir = "${params.condadir}"
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conda.channels = ['conda-forge', 'bioconda']
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// disable alternative executors
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apptainer.enabled = false
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charliecloud.enabled = false
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docker.enabled = false
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podman.enabled = false
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shifter.enabled = false
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singularity.enabled = false
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}
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conda {
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conda.enabled = true
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conda.cacheDir = "${params.condadir}"
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conda.channels = ['conda-forge', 'bioconda']
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// disable alternative executors
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apptainer.enabled = false
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charliecloud.enabled = false
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docker.enabled = false
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podman.enabled = false
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shifter.enabled = false
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singularity.enabled = false
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}
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mamba {
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conda.enabled = true
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conda.useMamba = true
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conda.cacheDir = "${params.condadir}"
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conda.channels = ['conda-forge', 'bioconda']
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// disable alternative executors
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apptainer.enabled = false
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charliecloud.enabled = false
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docker.enabled = false
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podman.enabled = false
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shifter.enabled = false
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singularity.enabled = false
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}
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apptainer {
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apptainer.enabled = true
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apptainer.autoMounts = true
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apptainer.cacheDir = "${params.singularity_cache}"
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apptainer.registry = params.registry ?: 'quay.io'
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apptainer.runOptions = "${params.container_opts}"
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// disable alternative executors
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charliecloud.enabled = false
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conda.enabled = false
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docker.enabled = false
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podman.enabled = false
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singularity.enabled = false
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shifter.enabled = false
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}
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charliecloud {
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charliecloud.enabled = true
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charliecloud.registry = params.registry ?: 'quay.io'
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// disable alternative executors
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apptainer.enabled = false
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conda.enabled = false
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docker.enabled = false
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podman.enabled = false
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shifter.enabled = false
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singularity.enabled = false
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}
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docker {
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docker.enabled = true
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docker.registry = params.registry ?: 'quay.io'
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docker.runOptions = '-u $(id -u):$(id -g) -v ${HOME}/.cache:/.cache -v ${HOME}/.config:/.config -v ${PWD}:/.medaka'
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// disable alternative executors
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apptainer.enabled = false
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charliecloud.enabled = false
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conda.enabled = false
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podman.enabled = false
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singularity.enabled = false
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shifter.enabled = false
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}
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arm {
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docker.enabled = true
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docker.registry = params.registry ?: 'quay.io'
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docker.runOptions = '-u $(id -u):$(id -g) -v ${HOME}/.cache:/.cache -v ${HOME}/.config:/.config -v ${PWD}:/.medaka --platform=linux/amd64'
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// disable alternative executors
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apptainer.enabled = false
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charliecloud.enabled = false
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conda.enabled = false
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podman.enabled = false
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singularity.enabled = false
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shifter.enabled = false
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}
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gitpod {
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executor.name = 'local'
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executor.cpus = 4
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executor.memory = 8.GB
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}
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podman {
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podman.enabled = true
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podman.registry = params.registry ?: 'quay.io'
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// disable alternative executors
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apptainer.enabled = false
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charliecloud.enabled = false
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conda.enabled = false
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docker.enabled = false
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shifter.enabled = false
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singularity.enabled = false
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}
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shifter {
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shifter.enabled = true
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// disable alternative executors
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apptainer.enabled = false
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conda.enabled = false
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docker.enabled = false
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podman.enabled = false
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charliecloud.enabled = false
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singularity.enabled = false
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}
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singularity {
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singularity.enabled = true
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singularity.autoMounts = true
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singularity.cacheDir = "${params.singularity_cache}"
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singularity.registry = params.registry ?: 'quay.io'
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singularity.runOptions = "${params.container_opts}"
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// disable alternative executors
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apptainer.enabled = false
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charliecloud.enabled = false
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conda.enabled = false
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docker.enabled = false
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podman.enabled = false
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shifter.enabled = false
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}
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wave {
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apptainer.ociAutoPull = true
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singularity.ociAutoPull = true
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wave.enabled = true
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wave.freeze = true
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wave.strategy = 'conda,container'
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}
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test { includeConfig './test.config' }
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}

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