hmmalign version bump. standardised output format, ported to nf-test

nf-core · Nov 13, 2024 · 8d30931 · 8d30931
1 parent 76fc14f
commit 8d30931
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Showing 6 changed files with 149 additions and 12 deletions.
diff --git a/modules/nf-core/hmmer/hmmalign/environment.yml b/modules/nf-core/hmmer/hmmalign/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::hmmer=3.3.2
+  - bioconda::hmmer=3.4
diff --git a/modules/nf-core/hmmer/hmmalign/main.nf b/modules/nf-core/hmmer/hmmalign/main.nf
@@ -4,16 +4,16 @@ process HMMER_HMMALIGN {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/hmmer:3.3.2--h1b792b2_1' :
-        'biocontainers/hmmer:3.3.2--h1b792b2_1' }"
+        'https://depot.galaxyproject.org/singularity/hmmer:3.4--hdbdd923_2' :
+        'biocontainers/hmmer:3.4--hdbdd923_2' }"
 
     input:
     tuple val(meta), path(fasta)
     path hmm
 
     output:
-    tuple val(meta), path("*.sthlm.gz"), emit: sthlm
-    path "versions.yml"                , emit: versions
+    tuple val(meta), path("*.sto.gz"), emit: sto
+    path "versions.yml"              , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -25,7 +25,18 @@ process HMMER_HMMALIGN {
     hmmalign \\
         $args \\
         $hmm \\
-        $fasta | gzip -c > ${prefix}.sthlm.gz
+        $fasta | gzip -c > ${prefix}.sto.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        hmmer: \$(hmmalign -h | grep -o '^# HMMER [0-9.]*' | sed 's/^# HMMER *//')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    echo | gzip > ${prefix}.sto.gz
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/nf-core/hmmer/hmmalign/meta.yml b/modules/nf-core/hmmer/hmmalign/meta.yml
@@ -30,16 +30,16 @@ input:
         description: A gzipped HMM file
         pattern: "*.hmm.gz"
 output:
-  - sthlm:
+  - sto:
       - meta:
           type: map
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - "*.sthlm.gz":
+      - "*.sto.gz":
           type: file
           description: Multiple alignment in gzipped Stockholm format
-          pattern: "*.sthlm.gz"
+          pattern: "*.sto.gz"
   - versions:
       - versions.yml:
           type: file
@@ -51,3 +51,4 @@ authors:
 maintainers:
   - "@erikrikarddaniel"
   - "@jfy133"
+  - "@vagkaratzas"
diff --git a/modules/nf-core/hmmer/hmmalign/tests/main.nf.test b/modules/nf-core/hmmer/hmmalign/tests/main.nf.test
@@ -0,0 +1,60 @@
+
+nextflow_process {
+
+    name "Test Process HMMER_HMMALIGN"
+    script "../main.nf"
+    process "HMMER_HMMALIGN"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "hmmer"
+    tag "hmmer/hmmalign"
+
+    test("test-hmmer-hmmalign") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id: 'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'delete_me/hmmer/e_coli_k12_16s.fna.gz', checkIfExists: true)
+				]
+				input[1] = file(params.modules_testdata_base_path + 'delete_me/hmmer/bac.16S_rRNA.hmm.gz', checkIfExists: true)
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test-hmmer-hmmalign-stub") {
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id: 'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'delete_me/hmmer/e_coli_k12_16s.fna.gz', checkIfExists: true)
+				]
+				input[1] = file(params.modules_testdata_base_path + 'delete_me/hmmer/bac.16S_rRNA.hmm.gz', checkIfExists: true)
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/hmmer/hmmalign/tests/main.nf.test.snap b/modules/nf-core/hmmer/hmmalign/tests/main.nf.test.snap
@@ -0,0 +1,68 @@
+{
+    "test-hmmer-hmmalign": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.sto.gz:md5,4ae989d5ade2aaae9578cb88ba031e8f"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,601e13e7a1e6057766d862a828d501c4"
+                ],
+                "sto": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.sto.gz:md5,4ae989d5ade2aaae9578cb88ba031e8f"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,601e13e7a1e6057766d862a828d501c4"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "23.04.5"
+        },
+        "timestamp": "2024-11-13T12:37:26.551497424"
+    },
+    "test-hmmer-hmmalign-stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.sto.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,601e13e7a1e6057766d862a828d501c4"
+                ],
+                "sto": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.sto.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,601e13e7a1e6057766d862a828d501c4"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "23.04.5"
+        },
+        "timestamp": "2024-11-13T12:37:32.244343836"
+    }
+}
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -299,9 +299,6 @@ hmmer/eslalimask:
 hmmer/eslreformat:
   - modules/nf-core/hmmer/eslreformat/**
   - tests/modules/nf-core/hmmer/eslreformat/**
-hmmer/hmmalign:
-  - modules/nf-core/hmmer/hmmalign/**
-  - tests/modules/nf-core/hmmer/hmmalign/**
 hmtnote/annotate:
   - modules/nf-core/hmtnote/annotate/**
   - tests/modules/nf-core/hmtnote/annotate/**