Update vrhyme modules, including nf-test

modules/nf-core/vrhyme/extractunbinned/main.nf

@@ -9,36 +9,45 @@ process VRHYME_EXTRACTUNBINNED {
 
     input:
     tuple val(meta), path(membership)
-    tuple val(meta), path(fasta)
+    tuple val(meta2), path(fasta)
 
     output:
-    tuple val(meta), path("*_unbinned_sequences.fasta") , emit: unbinned_sequences
-    path "versions.yml"                                 , emit: versions
+    tuple val(meta), path("${prefix}.fasta") , emit: unbinned_sequences
+    path "versions.yml"                      , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}_unbinned_sequences"
+    def fasta_input = fasta.toString().replaceAll(/\.gz$/, '')
+    def gunzip      = fasta.getExtension() == "gz" ? "gunzip -c ${fasta} > ${fasta_input}" : ""
+    def cleanup     = fasta.getExtension() == "gz" ? "rm ${fasta_input}" : ""
+    if( "$fasta_input" == "${prefix}.fasta" ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     """
+    ${gunzip}
+
     extract_unbinned_sequences.py \\
         -i $membership \\
-        -f $fasta \\
-        -o ${prefix}_unbinned_sequences.fasta \\
+        -f $fasta_input \\
+        -o ${prefix}.fasta \\
         $args
 
+    ${cleanup}
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         vrhyme: \$(echo \$(vRhyme --version 2>&1) | sed 's/^.*vRhyme v//; s/Using.*\$//' )
     END_VERSIONS
     """
 
     stub:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}_unbinned_sequences"
+    def fasta_input = fasta.toString() - ~/\.gz$/
+    if( "$fasta_input" == "${prefix}.fasta" ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     """
-    touch ${prefix}_unbinned_sequences.fasta
+    touch ${prefix}.fasta
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/nf-core/vrhyme/extractunbinned/meta.yml

@@ -22,32 +22,38 @@ input:
         type: map
         description: |
           Groovy Map containing sample information
-          e.g. [ id:'test', single_end:false ]
+          e.g. [ id:'test' ]
     - membership:
         type: file
         description: TSV file containing information regarding which bins input sequences
           were placed information
         pattern: "*.{tsv}"
-  - - meta:
+        ontologies:
+          - edam: http://edamontology.org/format_3475 # TSV
+  - - meta2:
         type: map
         description: |
-          Groovy Map containing sample information
-          e.g. [ id:'test', single_end:false ]
+          Groovy Map containing information related to the fasta
+          e.g. [ id:'test' ]
     - fasta:
         type: file
         description: FASTA file containing contigs/scaffolds input into vRhyme
-        pattern: "*.{fasta,fna,fa}"
+        pattern: "*.{fasta,fna,fa,fasta.gz,fna.gz,fa.gz}"
+        ontologies:
+          - edam: http://edamontology.org/format_1929 # FASTA
 output:
   - unbinned_sequences:
       - meta:
           type: map
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - "*_unbinned_sequences.fasta":
+      - "${prefix}.fasta":
           type: file
           description: FASTA file containing unbinned sequences
           pattern: "*_unbinned_sequences.fasta"
+          ontologies:
+          - edam: http://edamontology.org/format_1929 # FASTA
   - versions:
       - versions.yml:
           type: file

modules/nf-core/vrhyme/extractunbinned/tests/main.nf.test

@@ -0,0 +1,79 @@
+nextflow_process {
+
+    name "Test Process VRHYME_EXTRACTUNBINNED"
+
+    script "../main.nf"
+    process "VRHYME_EXTRACTUNBINNED"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "vrhyme"
+    tag "vrhyme/vrhyme"
+    tag "vrhyme/extractunbinned"
+
+    setup {
+
+        run("VRHYME_VRHYME") {
+            script "../../vrhyme/main.nf"
+
+            process {
+                """
+                input[0] = [
+                    [id:'test',single_end:false],
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_2.fastq.gz', checkIfExists: true)
+                    ]
+                ]
+                input[1] = [
+                    [id:'test',single_end:false],// meta map
+                        file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz', checkIfExists: true)
+                    ]
+                """
+            }
+        }
+    }
+
+    test("test_vrhyme_extractunbinned") {
+
+        when {
+            process {
+                """
+                input[0] = VRHYME_VRHYME.out.membership
+                input[1] = [
+                    [id:'test',single_end:false],// meta map
+                        file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz', checkIfExists: true)
+                    ]
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+
+    test("test_vrhyme_extractunbinned -- stub") {
+        options '-stub'
+        when {
+            process {
+                """
+                input[0] = VRHYME_VRHYME.out.membership
+                input[1] = [
+                    [id:'test',single_end:false],// meta map
+                        file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz', checkIfExists: true)
+                    ]
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}

modules/nf-core/vrhyme/extractunbinned/tests/main.nf.test.snap

@@ -0,0 +1,72 @@
+{
+    "test_vrhyme_extractunbinned -- stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_unbinned_sequences.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,19f257878bced6c770eaf8ed45151b96"
+                ],
+                "unbinned_sequences": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_unbinned_sequences.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,19f257878bced6c770eaf8ed45151b96"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-03-30T20:31:33.979555851"
+    },
+    "test_vrhyme_extractunbinned": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_unbinned_sequences.fasta:md5,816e986c8ad8f277eb4a4891a12d7aff"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,19f257878bced6c770eaf8ed45151b96"
+                ],
+                "unbinned_sequences": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_unbinned_sequences.fasta:md5,816e986c8ad8f277eb4a4891a12d7aff"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,19f257878bced6c770eaf8ed45151b96"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-03-31T10:00:14.099653894"
+    }
+}

modules/nf-core/vrhyme/linkbins/meta.yml

@@ -22,7 +22,7 @@ input:
         type: map
         description: |
           Groovy Map containing sample information
-          e.g. [ id:'test', single_end:false ]
+          e.g. [ id:'test' ]
     - bins:
         type: directory
         description: Directory file containing bin FASTA files output by vRhyme (each
@@ -38,11 +38,14 @@ output:
           type: file
           description: FASTA file containing all bins that have been linked by N's
           pattern: "*_linked_bins.fasta"
+          ontologies:
+            - edam: http://edamontology.org/format_1929 # FASTA
   - versions:
       - versions.yml:
           type: file
           description: File containing software versions
           pattern: "versions.yml"
+          ontologies: []
 authors:
   - "@CarsonJM"
 maintainers:

modules/nf-core/vrhyme/linkbins/tests/main.nf.test

@@ -0,0 +1,70 @@
+nextflow_process {
+
+    name "Test Process VRHYME_LINKBINS"
+
+    script "../main.nf"
+    process "VRHYME_LINKBINS"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "vrhyme"
+    tag "vrhyme/vrhyme"
+    tag "vrhyme/linkbins"
+
+    setup {
+        run("VRHYME_VRHYME") {
+            script "../../vrhyme/main.nf"
+
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_2.fastq.gz', checkIfExists: true)
+                    ]
+                    ]
+				input[1] = [
+				    [ id:'test' ],
+				    file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz', checkIfExists: true)
+				]
+                """
+            }
+        }
+    }
+
+    test("vrhyme_linkbins") {
+
+        when {
+            process {
+                """
+                input[0] = VRHYME_VRHYME.out.bins
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+
+    test("test_vrhyme_linkbins -- stub") {
+        options '-stub'
+        when {
+            process {
+                """
+                input[0] = VRHYME_VRHYME.out.bins
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}