Trycycler cluster (#5670)

* initial trycycler subsample commit * Update modules/nf-core/trycycler/subsample/main.nf to resolve issue with nf-test and empty gzipped files Co-authored-by: Simon Pearce <[email protected]> * addressing comments on initial commit, fixed version number, added stub tests * initial commit for trycycler cluster module --------- Co-authored-by: Simon Pearce <[email protected]>
nf-core · May 25, 2024 · e788348 · e788348
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diff --git a/modules/nf-core/trycycler/cluster/environment.yml b/modules/nf-core/trycycler/cluster/environment.yml
@@ -0,0 +1,9 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "trycycler_cluster"
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - "bioconda::trycycler=0.5.3"
diff --git a/modules/nf-core/trycycler/cluster/main.nf b/modules/nf-core/trycycler/cluster/main.nf
@@ -0,0 +1,56 @@
+process TRYCYCLER_CLUSTER {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/trycycler:0.5.3--pyhdfd78af_0':
+        'biocontainers/trycycler:0.5.3--pyhdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(contigs), path(reads)
+
+    output:
+    tuple val(meta), path("*") , emit: cluster_dir
+    path "versions.yml"        , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def args2 = task.ext.args2 ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    trycycler \\
+        cluster \\
+        $args \\
+        --assemblies ${contigs} \\
+        --reads ${reads} \\
+        --threads $task.cpus \\
+        --out_dir ${prefix}
+
+    gzip $args2 ${prefix}/cluster_*/*/*.fasta
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        trycycler: \$(trycycler --version | sed 's/Trycycler v//')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    mkdir -p ${prefix}/cluster_001/1_contigs
+    echo "" | gzip > ${prefix}/cluster_001/1_contigs/A_contig_2a.fasta.gz
+    touch ${prefix}/contigs.newick
+    touch ${prefix}/contigs.phylip
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        trycycler: \$(trycycler --version | sed 's/Trycycler v//')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/trycycler/cluster/meta.yml b/modules/nf-core/trycycler/cluster/meta.yml
@@ -0,0 +1,55 @@
+name: "trycycler_cluster"
+description: Cluster contigs from multiple assemblies by similarity
+keywords:
+  - cluster
+  - alignment
+  - fastq
+  - fasta
+  - genomics
+tools:
+  - "trycycler":
+      description: Trycycler is a tool for generating consensus long-read assemblies for bacterial genomes
+      homepage: https://github.com/rrwick/Trycycler
+      documentation: https://github.com/rrwick/Trycycler/wiki
+      doi: 10.1186/s13059-021-02483-z
+      licence: ["GPL v3"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+
+  - reads:
+      type: file
+      description: Long-read FASTQ file, optionally gzip compressed
+
+  - assemblies:
+      type: file
+      description: Input assemblies whose contigs will be clustered
+
+  - out_dir:
+      type: directory
+      description: Output directory for clustering results
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+
+  - cluster_dir:
+      type: directory
+      description: Output directory containing clustering results
+
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@watsonar"
+maintainers:
+  - "@watsonar"
diff --git a/modules/nf-core/trycycler/cluster/tests/main.nf.test b/modules/nf-core/trycycler/cluster/tests/main.nf.test
@@ -0,0 +1,77 @@
+nextflow_process {
+
+    name "Test Process TRYCYCLER_CLUSTER"
+    script "../main.nf"
+    process "TRYCYCLER_CLUSTER"
+    config './nextflow.config'
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "trycycler"
+    tag "trycycler/cluster"
+
+    test("custom test data") {
+
+        when {
+            process {
+                """
+                def contigs1 = file("contigs1.fasta")
+                contigs1.text = '>contig_1a\\nATCCCCTTGGACTCCTAGCTAGGCTCTAGAGCCTTCTCTCGACTACGAGCTAGCAGCTACGATCACGACTACAGCACAGCACTACAGCATCAGCACAGCAGTCAGCGA\\n>contig_2a\\nGCTAGGCTCTAACGCGCCATCAGCCGCTCAGCTACGACTATCGCAGCTACGATCAGCATCGATCTAGCAGAGCCTTCTGGTAACGCGACTCAGTCTCTACAGCACGGTAACCAGCACTACAGGGGTTAAGCCCATCA\\n'
+
+                def contigs2 = file("contigs2.fasta")
+                contigs2.text = '>contig_1b\\nATCCCCTTGGACTCCTAGCTAGGCTCTAGAGCCTTCTCTCGACTACCCAGCTAGCAGCTACGATCACGTCTACAGCACAGCACTACAGCATCAGCACAGCAGTA\\n>contig_2b\\nGCTAGGCTCTAACGCGCCATCAGCCGCTCAGCTACGACTAGCGCAGCTACGATCAGCATCCATCTAGCAGAGCCAACTGGTAACGCGACTCAGTCTCTACAGCACGGTAACCAGCACTACAGGGGTTAAGCCCATCA\\n'
+
+                def reads = file("reads.fastq")
+                reads.text = '@NC-000913.3_646515_unaligned_0_F_0_1238_0\\nCTCTAGAGCCTTCTCTCGACTACGAGCTAGCAGCTACGA\\n+\\nIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\\[email protected]_646518_unaligned_0_F_0_1238_0\\nTAGGCTCTAACGCGCCATCAGCCGCTCAGCTACGACTAGCGC\\n+\\nIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\\n'
+
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    [ file('contigs1.fasta', checkIfExists: true), file('contigs2.fasta', checkIfExists: true) ], // contigs
+                    file('reads.fastq', checkIfExists: true) // reads
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("custom test data - stub") {
+
+        when {
+            process {
+                options "-stub-run"
+                """
+                def contigs1 = file("contigs1.fasta")
+                contigs1.text = '>contig_1a\\nATCCCCTTGGACTCCTAGCTAGGCTCTAGAGCCTTCTCTCGACTACGAGCTAGCAGCTACGATCACGACTACAGCACAGCACTACAGCATCAGCACAGCAGTCAGCGA\\n>contig_2a\\nGCTAGGCTCTAACGCGCCATCAGCCGCTCAGCTACGACTATCGCAGCTACGATCAGCATCGATCTAGCAGAGCCTTCTGGTAACGCGACTCAGTCTCTACAGCACGGTAACCAGCACTACAGGGGTTAAGCCCATCA\\n'
+
+                def contigs2 = file("contigs2.fasta")
+                contigs2.text = '>contig_1b\\nATCCCCTTGGACTCCTAGCTAGGCTCTAGAGCCTTCTCTCGACTACCCAGCTAGCAGCTACGATCACGTCTACAGCACAGCACTACAGCATCAGCACAGCAGTA\\n>contig_2b\\nGCTAGGCTCTAACGCGCCATCAGCCGCTCAGCTACGACTAGCGCAGCTACGATCAGCATCCATCTAGCAGAGCCAACTGGTAACGCGACTCAGTCTCTACAGCACGGTAACCAGCACTACAGGGGTTAAGCCCATCA\\n'
+
+                def reads = file("reads.fastq")
+                reads.text = '@NC-000913.3_646515_unaligned_0_F_0_1238_0\\nCTCTAGAGCCTTCTCTCGACTACGAGCTAGCAGCTACGA\\n+\\nIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\\[email protected]_646518_unaligned_0_F_0_1238_0\\nTAGGCTCTAACGCGCCATCAGCCGCTCAGCTACGACTAGCGC\\n+\\nIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\\n'
+
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    [ file('contigs1.fasta', checkIfExists: true), file('contigs2.fasta', checkIfExists: true) ], // contigs
+                    file('reads.fastq', checkIfExists: true) // reads
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+}
diff --git a/modules/nf-core/trycycler/cluster/tests/main.nf.test.snap b/modules/nf-core/trycycler/cluster/tests/main.nf.test.snap
@@ -0,0 +1,142 @@
+{
+    "custom test data - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            [
+                                [
+                                    [
+                                        "A_contig_2a.fasta.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                                    ]
+                                ],
+                                "contigs.newick:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                "contigs.phylip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                            ],
+                            "versions.yml:md5,616584ce01fb659316a99b1329e047aa"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,616584ce01fb659316a99b1329e047aa"
+                ],
+                "cluster_dir": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            [
+                                [
+                                    [
+                                        "A_contig_2a.fasta.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                                    ]
+                                ],
+                                "contigs.newick:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                "contigs.phylip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                            ],
+                            "versions.yml:md5,616584ce01fb659316a99b1329e047aa"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,616584ce01fb659316a99b1329e047aa"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-22T14:59:36.502272455"
+    },
+    "custom test data": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            [
+                                [
+                                    [
+                                        "A_contig_2a.fasta.gz:md5,2c579f9cc210a544772daa7f4a16d0d5"
+                                    ]
+                                ],
+                                [
+                                    [
+                                        "B_contig_2b.fasta.gz:md5,4b4819e6b8f996d387216450b314798e"
+                                    ]
+                                ],
+                                [
+                                    [
+                                        "A_contig_1a.fasta.gz:md5,6d49552461c330871cecac80635c1798"
+                                    ]
+                                ],
+                                [
+                                    [
+                                        "B_contig_1b.fasta.gz:md5,f012c88fa34c176735737485eb730d71"
+                                    ]
+                                ],
+                                "contigs.newick:md5,1793ccb2bff4a79525a1ce60fb90f8ab",
+                                "contigs.phylip:md5,984639efc8ae4b4cbe6e53bdb0b8b8c1"
+                            ],
+                            "versions.yml:md5,616584ce01fb659316a99b1329e047aa"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,616584ce01fb659316a99b1329e047aa"
+                ],
+                "cluster_dir": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            [
+                                [
+                                    [
+                                        "A_contig_2a.fasta.gz:md5,2c579f9cc210a544772daa7f4a16d0d5"
+                                    ]
+                                ],
+                                [
+                                    [
+                                        "B_contig_2b.fasta.gz:md5,4b4819e6b8f996d387216450b314798e"
+                                    ]
+                                ],
+                                [
+                                    [
+                                        "A_contig_1a.fasta.gz:md5,6d49552461c330871cecac80635c1798"
+                                    ]
+                                ],
+                                [
+                                    [
+                                        "B_contig_1b.fasta.gz:md5,f012c88fa34c176735737485eb730d71"
+                                    ]
+                                ],
+                                "contigs.newick:md5,1793ccb2bff4a79525a1ce60fb90f8ab",
+                                "contigs.phylip:md5,984639efc8ae4b4cbe6e53bdb0b8b8c1"
+                            ],
+                            "versions.yml:md5,616584ce01fb659316a99b1329e047aa"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,616584ce01fb659316a99b1329e047aa"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-22T14:59:28.088111496"
+    }
+}
diff --git a/modules/nf-core/trycycler/cluster/tests/nextflow.config b/modules/nf-core/trycycler/cluster/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: TRYCYCLER_CLUSTER {
+        ext.args = '--min_contig_len 0 --min_contig_depth 0'
+    }
+}
diff --git a/modules/nf-core/trycycler/cluster/tests/tags.yml b/modules/nf-core/trycycler/cluster/tests/tags.yml
@@ -0,0 +1,2 @@
+trycycler/cluster:
+  - "modules/nf-core/trycycler/cluster/**"
diff --git a/modules/nf-core/trycycler/subsample/environment.yml b/modules/nf-core/trycycler/subsample/environment.yml
@@ -0,0 +1,9 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "trycycler_subsample"
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - "bioconda::trycycler=0.5.3"