Update learnmsa

modules/nf-core/learnmsa/align/environment.yml

@@ -2,5 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::learnmsa=2.0.1
-  - conda-forge::pigz=2.8
+  - conda-forge::coreutils=9.5

modules/nf-core/learnmsa/align/main.nf

@@ -1,50 +1,45 @@
 process LEARNMSA_ALIGN {
     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/mulled-v2-741e0da5cf2d6d964f559672e2908c2111cbb46b:4930edd009376542543bfd2e20008bb1ae58f841-0' :
-        'biocontainers/mulled-v2-741e0da5cf2d6d964f559672e2908c2111cbb46b:4930edd009376542543bfd2e20008bb1ae58f841-0' }"
+    container "registry.hub.docker.com/felbecker/learnmsa:2.0.9"
 
     input:
     tuple val(meta), path(fasta)
-    val(compress)
 
     output:
-    tuple val(meta), path("*.aln{.gz,}"), emit: alignment
+    tuple val(meta), path("*.aln")      , emit: alignment
     path "versions.yml"                 , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
+    def args   = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def write_output = compress ? ">(pigz -cp ${task.cpus} > ${prefix}.aln.gz)" : "${prefix}.aln"
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error("LearnMSA align module does not support Conda. Please use Docker / Singularity / Podman instead.")
+    }
     """
     learnMSA \\
-        $args \\
-        -i <(unpigz -cdf $fasta) \\
-        -o $write_output
+        -i $fasta \\
+        -o "${prefix}.aln" \\
+        $args
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         learnmsa: \$(learnMSA -h | grep 'version' | awk -F 'version ' '{print \$2}' | awk '{print \$1}' | sed 's/)//g')
-        pigz: \$(echo \$(pigz --version 2>&1) | sed 's/^.*pigz\\w*//' ))
     END_VERSIONS
     """
 
     stub:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${prefix}.aln${compress ? '.gz' : ''}
+    touch ${prefix}.aln
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        learnmsa: \$(learnMSA -h | grep 'version' | awk -F 'version ' '{print \$2}' | awk '{print \$1}' | sed 's/)//g')
-        pigz: \$(echo \$(pigz --version 2>&1) | sed 's/^.*pigz\\w*//' ))
+        learnmsa: \$(if command -v learnMSA &>/dev/null; then learnMSA -h | grep 'version' | awk -F 'version ' '{print \$2}' | awk '{print \$1}' | sed 's/)//g'; else echo "STUB_TEST_HARDCODED_VERSION"; fi)
     END_VERSIONS
     """
 }

modules/nf-core/learnmsa/align/meta.yml

@@ -21,24 +21,19 @@ input:
           e.g. `[ id:'test']`
     - fasta:
         type: file
-        description: Input sequences in FASTA format. May be gz-compressed or uncompressed.
-        pattern: "*.{fa,fasta}{.gz,}"
-  - - compress:
-        type: boolean
-        description: Flag representing whether the output MSA should be compressed.
-          Set to true to enable/false to disable compression. Compression is done using
-          pigz, and is multithreaded.
+        description: Input sequences in FASTA format.
+        pattern: "*.{fa,fasta}"
 output:
   - alignment:
       - meta:
           type: map
           description: |
             Groovy Map containing sample information
             e.g. `[ id:'test']`
-      - "*.aln{.gz,}":
+      - "*.aln":
           type: file
-          description: Alignment file, in FASTA format. May be gzipped or uncompressed.
-          pattern: "*.aln{.gz,}"
+          description: Alignment file, in FASTA format.
+          pattern: "*.aln"
   - versions:
       - versions.yml:
           type: file

modules/nf-core/learnmsa/align/tests/main.nf.test

@@ -2,6 +2,7 @@
 nextflow_process {
 
     name "Test Process LEARNMSA_ALIGN"
+    config "./nextflow.config"
     script "../main.nf"
     process "LEARNMSA_ALIGN"
 
@@ -10,47 +11,24 @@ nextflow_process {
     tag "learnmsa"
     tag "learnmsa/align"
 
-    test("sarscov2 - fasta - uncompressed") {
+    test("seatoxin - stub") {
+        options "-stub"
 
         when {
             process {
                 """
-                input[0] = [ [ id:'test' ], // meta map
-                             file(params.test_data['sarscov2']['genome']['informative_sites_fas'], checkIfExists: true)
+                input[0] = [ [ id:'test' ],
+                             file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true)
                            ]
-                input[1] = false
                 """
             }
         }
 
         then {
             assertAll(
                 { assert process.success },
-                { assert path(process.out.alignment.get(0).get(1)).getText().contains(">sample1") },
-                { assert snapshot(process.out.versions).match("versions") }
-            )
-        }
-
-    }
-
-    test("sarscov2 - fasta - compressed") {
-
-        when {
-            process {
-                """
-                input[0] = [ [ id:'test' ], // meta map
-                             file(params.test_data['sarscov2']['genome']['informative_sites_fas'], checkIfExists: true)
-                           ]
-                input[1] = true
-                """
-            }
-        }
+                { assert snapshot ( process.out ).match() }
 
-        then {
-            assertAll(
-                { assert process.success },
-                { assert path(process.out.alignment.get(0).get(1)).getTextGzip().contains(">sample1") },
-                { assert snapshot(process.out.versions).match("versions1") }
             )
         }
 

modules/nf-core/learnmsa/align/tests/main.nf.test.snap

@@ -1,26 +1,35 @@
 {
-    "versions": {
+    "seatoxin - stub": {
         "content": [
-            [
-                "versions.yml:md5,85322b0f038aa768f202fd0d748d6c7c"
-            ]
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.aln:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,c3886d32309d141ad22aba3a8a119d62"
+                ],
+                "alignment": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.aln:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,c3886d32309d141ad22aba3a8a119d62"
+                ]
+            }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-03-20T16:06:48.867020809"
-    },
-    "versions1": {
-        "content": [
-            [
-                "versions.yml:md5,85322b0f038aa768f202fd0d748d6c7c"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-03-20T16:12:13.921813607"
+        "timestamp": "2025-01-31T13:29:53.669503397"
     }
 }

modules/nf-core/learnmsa/align/tests/nextflow.config

@@ -0,0 +1,7 @@
+process {
+
+    withName: LEARNMSA_ALIGN{
+        container = "nf-core/ubuntu:22.04"
+    }
+
+}