Add Autocycler subtool modules (subsample, compress, cluster, trim, resolve, combine)

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

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+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::autocycler=0.5.2"

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

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

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

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

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

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+nextflow_process {
+
+    name "Test Process AUTOCYCLER_CLUSTER"
+    script "../main.nf"
+    process "AUTOCYCLER_CLUSTER"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "autocycler"
+    tag "autocycler/compress"
+    tag "autocycler/cluster"
+
+    test("sarscov2 - assembly - fasta") {
+
+        setup {
+            run("AUTOCYCLER_COMPRESS") {
+                script "../../compress/main.nf"
+                process {
+                    """
+                    input[0] = [
+                        [ id:'test', single_end:false ], // meta map
+                        [
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true),
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/scaffolds.fasta', checkIfExists: true),
+                        ] // assemblies
+                    ]
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = AUTOCYCLER_COMPRESS.out.gfa
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - assembly - fasta - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    []
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}