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Add autocycler modules
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‎modules/nf-core/autocycler/cluster/environment.yml‎

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---
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# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
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channels:
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- conda-forge
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- bioconda
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dependencies:
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# TODO nf-core: List required Conda package(s).
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# Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
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# For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
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- "bioconda::autocycler=0.5.2"

‎modules/nf-core/autocycler/cluster/main.nf‎

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process AUTOCYCLER_CLUSTER {
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tag "$meta.id"
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label 'process_low'
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conda "${moduleDir}/environment.yml"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/autocycler:0.5.2--h3ab6199_0':
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'biocontainers/autocycler:0.5.2--h3ab6199_0' }"
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input:
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tuple val(meta), path(gfa)
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output:
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tuple val(meta), path("clustering/qc_pass/*/*.gfa"), emit: clusters
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tuple val(meta), path("clustering/qc_pass/*/*.yaml"), emit: clusterstats
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tuple val(meta), path("clustering/*.newick"), emit: newick
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tuple val(meta), path("clustering/*.tsv"), emit: tsv
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tuple val(meta), path("clustering/*.phylip"), emit: pairwisedistances
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tuple val(meta), path("clustering/*.yaml"), emit: stats
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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autocycler cluster \\
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$args \\
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-a .
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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autocycler: \$(autocycler --version | sed 's/^[^ ]* //')
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END_VERSIONS
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"""
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stub:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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mkdir clustering/qc_pass/cluster_000 -p
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touch clustering.{newick,yaml,tsv}
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touch pairwise_distances.phylip
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touch clustering/qc_pass/cluster_000/0_untrimmed.{gfa,yaml}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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autocycler: \$(autocycler --version | sed 's/^[^ ]* //')
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END_VERSIONS
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"""
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}

‎modules/nf-core/autocycler/cluster/meta.yml‎

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---
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# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
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name: "autocycler_cluster"
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description: Cluster replicons in compressed assemblies with Autocycler.
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keywords:
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- autocycler
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- genome-assembly
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- clustering
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- long-read
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tools:
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- autocycler:
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description: "A tools for generating consensus long-read assemblies for bacterial genomes."
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homepage: "https://github.com/rrwick/Autocycler/wiki"
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documentation: "https://github.com/rrwick/Autocycler/wiki"
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tool_dev_url: "https://github.com/rrwick/Autocycler"
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doi: "10.1093/bioinformatics/btaf474"
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licence: ["GPL-3.0"]
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input:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. `[ id:'sample1' ]`
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- gfa:
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type: file
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description: |
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Assembly graph files produced by the compression step.
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pattern: "*/*.gfa"
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output:
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clusters:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. `[ id:'sample1' ]`
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- "clustering/qc_pass/*/*.gfa":
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type: file
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description: Aassembly graphs of clustered contigs.
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pattern: "clustering/qc_pass/*/*.gfa"
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ontologies:
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- edam: "http://edamontology.org/format_3975" #GFA1
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clusterstats:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. `[ id:'sample1' ]`
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- "clustering/qc_pass/*/*.yaml":
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type: file
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description: Per-cluster metrics reported by Autocycler.
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pattern: "clustering/qc_pass/*/*.yaml"
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ontologies:
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- edam: "http://edamontology.org/format_3750" # YAML
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newick:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. `[ id:'sample1' ]`
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- "clustering/*.newick":
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type: file
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description: Newick tree relating contigs.
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pattern: "clustering/*.newick"
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tsv:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. `[ id:'sample1' ]`
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- "clustering/*.tsv":
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type: file
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description: Tabular summary of cluster relationships.
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pattern: "clustering/*.tsv"
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pairwisedistances:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. `[ id:'sample1' ]`
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- "clustering/*.phylip":
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type: file
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description: Pairwise distance matrix in PHYLIP format.
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pattern: "clustering/*.phylip"
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stats:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. `[ id:'sample1' ]`
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- "clustering/*.yaml":
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type: file
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description: Run-level statistics for the clustering step.
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pattern: "clustering/*.yaml"
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ontologies:
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- edam: "http://edamontology.org/format_3750" # YAML
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versions:
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- "versions.yml":
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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ontologies:
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- edam: "http://edamontology.org/format_3750" # YAML
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authors:
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- "@dwells-eit"
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maintainers:
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- "@dwells-eit"

‎modules/nf-core/autocycler/cluster/tests/main.nf.test‎

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// TODO nf-core: Once you have added the required tests, please run the following command to build this file:
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// nf-core modules test autocycler/cluster
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nextflow_process {
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name "Test Process AUTOCYCLER_CLUSTER"
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script "../main.nf"
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process "AUTOCYCLER_CLUSTER"
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tag "modules"
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tag "modules_"
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tag "autocycler"
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tag "autocycler/cluster"
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// TODO nf-core: Change the test name preferably indicating the test-data and file-format used
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test("sarscov2 - bam") {
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// TODO nf-core: If you are created a test for a chained module
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// (the module requires running more than one process to generate the required output)
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// add the 'setup' method here.
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// You can find more information about how to use a 'setup' method in the docs (https://nf-co.re/docs/contributing/modules#steps-for-creating-nf-test-for-chained-modules).
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when {
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process {
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"""
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// TODO nf-core: define inputs of the process here. Example:
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input[0] = [
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[ id:'test', single_end:false ], // meta map
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file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
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]
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"""
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}
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}
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then {
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assertAll(
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{ assert process.success },
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{ assert snapshot(process.out).match() }
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//TODO nf-core: Add all required assertions to verify the test output.
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// See https://nf-co.re/docs/contributing/tutorials/nf-test_assertions for more information and examples.
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)
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}
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}
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// TODO nf-core: Change the test name preferably indicating the test-data and file-format used but keep the " - stub" suffix.
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test("sarscov2 - bam - stub") {
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options "-stub"
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when {
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process {
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"""
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// TODO nf-core: define inputs of the process here. Example:
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input[0] = [
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[ id:'test', single_end:false ], // meta map
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file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
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]
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"""
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}
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}
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then {
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assertAll(
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{ assert process.success },
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{ assert snapshot(process.out).match() }
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//TODO nf-core: Add all required assertions to verify the test output.
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)
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}
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}
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}

‎modules/nf-core/autocycler/combine/environment.yml‎

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---
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# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
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channels:
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- conda-forge
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- bioconda
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dependencies:
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# TODO nf-core: List required Conda package(s).
8+
# Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
9+
# For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
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- "bioconda::autocycler=0.5.2"

‎modules/nf-core/autocycler/combine/main.nf‎

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process AUTOCYCLER_COMBINE {
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tag "$meta.id"
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label 'process_single'
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conda "${moduleDir}/environment.yml"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/autocycler:0.5.2--h3ab6199_0':
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'biocontainers/autocycler:0.5.2--h3ab6199_0' }"
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input:
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tuple val(meta), path(clusters)
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output:
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tuple val(meta), path("$prefix/consensus_assembly.fasta"), emit: fasta
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tuple val(meta), path("$prefix/consensus_assembly.gfa"), emit: gfa
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tuple val(meta), path("$prefix/consensus_assembly.yaml"), emit: stats
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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prefix = task.ext.prefix ?: "${meta.id}"
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"""
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autocycler combine \\
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$args \\
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-i $clusters \\
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-a $prefix
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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autocycler: \$(autocycler --version | sed 's/^[^ ]* //')
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END_VERSIONS
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"""
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stub:
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def args = task.ext.args ?: ''
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prefix = task.ext.prefix ?: "${meta.id}"
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"""
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mkdir $prefix
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touch $prefix/consensus_assembly.{fasta,gfa,yaml}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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autocycler: \$(autocycler --version | sed 's/^[^ ]* //')
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END_VERSIONS
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"""
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}

‎modules/nf-core/autocycler/combine/meta.yml‎

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---
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# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
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name: "autocycler_combine"
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description: Merge resolved cluster assemblies into final consensus outputs with Autocycler.
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keywords:
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- autocycler
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- genome-assembly
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- consensus
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- long-read
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tools:
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- autocycler:
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description: "A tools for generating consensus long-read assemblies for bacterial genomes."
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homepage: "https://github.com/rrwick/Autocycler/wiki"
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documentation: "https://github.com/rrwick/Autocycler/wiki"
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tool_dev_url: "https://github.com/rrwick/Autocycler"
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doi: "10.1093/bioinformatics/btaf474"
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licence: ["GPL-3.0"]
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input:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. `[ id:'sample1' ]`
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- clusters:
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type: file
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description: |
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Final cluster assembly graphs (GFA) to be combined into consensus sequences.
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pattern: "*.gfa"
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output:
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fasta:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. `[ id:'sample1' ]`
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- "*/consensus_assembly.fasta":
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type: file
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description: Consensus genome sequence generated by Autocycler.
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pattern: "*/consensus_assembly.fasta"
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ontologies:
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- edam: "http://edamontology.org/format_1929" # FASTA
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gfa:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. `[ id:'sample1' ]`
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- "*/consensus_assembly.gfa":
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type: file
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description: Consensus assembly graph generated by Autocycler.
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pattern: "*/consensus_assembly.gfa"
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ontologies:
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- edam: "http://edamontology.org/format_3975" #GFA1 stats:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. `[ id:'sample1' ]`
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- "*/consensus_assembly.yaml":
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type: file
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description: Run statistics for the combine step.
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pattern: "*/consensus_assembly.yaml"
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ontologies:
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- edam: "http://edamontology.org/format_3750" # YAML
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versions:
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- "versions.yml":
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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ontologies:
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- edam: "http://edamontology.org/format_3750" # YAML
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authors:
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- "@dwells-eit"
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maintainers:
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- "@dwells-eit"

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