Allow Metabat2 to take uncompressed depths file and bump version (nf-…

…core#7230) * Metabat2 takes uncompressed depths file * Update main.nf.test * Update main.nf * Update environment.yml * update snapshot * Move shared setup outside of test blocks to facilitate reuse, switch to regex for cleaning depths
atrigila · Dec 19, 2024 · cc217b9 · cc217b9
1 parent 8581a56
commit cc217b9
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Showing 4 changed files with 70 additions and 27 deletions.
diff --git a/modules/nf-core/metabat2/metabat2/environment.yml b/modules/nf-core/metabat2/metabat2/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::metabat2=2.15
+  - bioconda::metabat2=2.17
diff --git a/modules/nf-core/metabat2/metabat2/main.nf b/modules/nf-core/metabat2/metabat2/main.nf
@@ -4,8 +4,8 @@ process METABAT2_METABAT2 {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/metabat2:2.15--h986a166_1' :
-        'biocontainers/metabat2:2.15--h986a166_1' }"
+        'https://depot.galaxyproject.org/singularity/metabat2:2.17--hd498684_0' :
+        'biocontainers/metabat2:2.17--hd498684_0' }"
 
     input:
     tuple val(meta), path(fasta), path(depth)
@@ -24,15 +24,16 @@ process METABAT2_METABAT2 {
     script:
     def args             = task.ext.args   ?: ''
     def prefix           = task.ext.prefix ?: "${meta.id}"
-    def decompress_depth = depth           ? "gzip -d -f $depth"    : ""
-    def depth_file       = depth           ? "-a ${depth.baseName}" : ""
+    def clean_depth      = depth.toString() - ~/\.gz$/
+    def decompress_depth = (depth && depth.toString() != clean_depth) ? "gzip -d -f $depth" : ""
+    def depth_input      = depth ? "-a ${clean_depth}" : ""
     """
     $decompress_depth
 
     metabat2 \\
-        $args \\
+        ${args} \\
         -i $fasta \\
-        $depth_file \\
+        ${depth_input} \\
         -t $task.cpus \\
         --saveCls \\
         -o ${prefix}

diff --git a/modules/nf-core/metabat2/metabat2/tests/main.nf.test b/modules/nf-core/metabat2/metabat2/tests/main.nf.test
@@ -7,10 +7,35 @@ nextflow_process {
 
     tag "modules"
     tag "modules_nfcore"
+    tag "gunzip"
     tag "metabat2"
     tag "metabat2/metabat2"
     tag "metabat2/jgisummarizebamcontigdepths"
 
+    setup {
+        run("METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS") {
+            script "../../jgisummarizebamcontigdepths/main.nf"
+            process {
+                """
+                input[0] = [
+                                [id: 'test', single_end: false],
+                                file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                                file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+                            ]
+                """
+            }
+        }
+
+        run("GUNZIP") {
+            script "../../../gunzip/main.nf"
+            process {
+                """
+                input[0] = METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS.out.depth
+                """
+            }
+        }
+    }
+
     test("sarscov2 - genome - fasta") {
 
         when {
@@ -36,28 +61,35 @@ nextflow_process {
 
     test("sarscov2 - genome - fasta - depths") {
 
-        setup {
-            run("METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS") {
-                script "../../jgisummarizebamcontigdepths/main.nf"
-                process {
-                    """
-                    input[0] = [
-                                    [id: 'test', single_end: false],
-                                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
-                                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
-                                ]
-                    """
-                }
+        when {
+            process {
+                """
+                input[0] = Channel
+                            .fromPath(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                            .map { it -> [[ id:'test', single_end:false ], it] }
+                            .join(METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS.out.depth)
+                """
             }
         }
 
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(file(process.out.membership[0][1]).name).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - genome - fasta - depths uncompressed") {
+
         when {
             process {
                 """
                 input[0] = Channel
                             .fromPath(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                             .map { it -> [[ id:'test', single_end:false ], it] }
-                            .join(METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS.out.depth)
+                            .join(GUNZIP.out.gunzip)
                 """
             }
         }

diff --git a/modules/nf-core/metabat2/metabat2/tests/main.nf.test.snap b/modules/nf-core/metabat2/metabat2/tests/main.nf.test.snap
@@ -24,7 +24,7 @@
 
                 ],
                 "5": [
-                    "versions.yml:md5,872d18278c2ba7812c62a8bc6b2120eb"
+                    "versions.yml:md5,f5ad39cc43905d8b2c61bf04772a1bda"
                 ],
                 "fasta": [
 
@@ -48,15 +48,25 @@
 
                 ],
                 "versions": [
-                    "versions.yml:md5,872d18278c2ba7812c62a8bc6b2120eb"
+                    "versions.yml:md5,f5ad39cc43905d8b2c61bf04772a1bda"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2024-12-11T12:28:01.970872008"
+        "timestamp": "2024-12-16T18:47:12.382730533"
+    },
+    "sarscov2 - genome - fasta - depths uncompressed": {
+        "content": [
+            "test.tsv.gz"
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-16T17:07:33.15263136"
     },
     "sarscov2 - genome - fasta - depths": {
         "content": [
@@ -66,7 +76,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2024-12-11T13:08:47.777561763"
+        "timestamp": "2024-12-16T17:07:19.028059191"
     },
     "sarscov2 - genome - fasta - stub": {
         "content": [
@@ -117,7 +127,7 @@
                     ]
                 ],
                 "5": [
-                    "versions.yml:md5,872d18278c2ba7812c62a8bc6b2120eb"
+                    "versions.yml:md5,f5ad39cc43905d8b2c61bf04772a1bda"
                 ],
                 "fasta": [
                     [
@@ -165,14 +175,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,872d18278c2ba7812c62a8bc6b2120eb"
+                    "versions.yml:md5,f5ad39cc43905d8b2c61bf04772a1bda"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2024-12-11T12:28:32.122007408"
+        "timestamp": "2024-12-16T18:48:01.719015314"
     }
 }