BBMAP/repair snapshot added

nf-core · Dec 19, 2024 · dd2a11a · dd2a11a
1 parent 14dcd6b
commit dd2a11a
Show file tree

Hide file tree

Showing 6 changed files with 188 additions and 31 deletions.
diff --git a/modules/nf-core/bbmap/repair/environment.yml b/modules/nf-core/bbmap/repair/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::bbmap=39.10"
+  - "bioconda::bbmap=39.13"
diff --git a/modules/nf-core/bbmap/repair/main.nf b/modules/nf-core/bbmap/repair/main.nf
@@ -3,8 +3,8 @@ process BBMAP_REPAIR {
     label 'process_single'
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bbmap:39.10--h92535d8_0':
-        'biocontainers/bbmap:39.10--h92535d8_0' }"
+        'https://depot.galaxyproject.org/singularity/bbmap:39.13--he5f24ec_1':
+        'biocontainers/bbmap:39.13--he5f24ec_1' }"
 
     input:
     tuple val(meta), path(reads)
@@ -21,10 +21,10 @@ process BBMAP_REPAIR {
 
     script:
     def args   = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    def in_reads  = ( interleave )  ? "in=${reads[0]}" : "in=${reads[0]} in2=${reads[1]}"
-    def out_reads = ( interleave )  ? "out=${prefix}_repaired.fastq.gz outs=${prefix}_singleton.fastq.gz"
-                                    : "out=${prefix}_1_repaired.fastq.gz out2=${prefix}_2_repaired.fastq.gz outs=${prefix}_singleton.fastq.gz"
+    prefix = task.ext.prefix ?: "${meta.id}"
+    in_reads  = ( interleave )  ? "in=${reads[0]}" : "in=${reads[0]} in2=${reads[1]}"
+    out_reads = ( interleave )  ? "out=${prefix}_repaired.fastq.gz outs=${prefix}_singleton.fastq.gz"
+                                : "out=${prefix}_1_repaired.fastq.gz out2=${prefix}_2_repaired.fastq.gz outs=${prefix}_singleton.fastq.gz"
     """
     maxmem=\$(echo \"$task.memory\"| sed 's/ GB/g/g')
     repair.sh \\
@@ -42,11 +42,7 @@ process BBMAP_REPAIR {
     """
 
     stub:
-    def args   = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    def in_reads  = ( args.interleave ) ? "in=${reads[0]}" : "in=${reads[0]} in2=${reads[1]}"
-    def out_reads = ( args.interleave ) ? "out=${prefix}_repaired.fastq.gz outs=${prefix}_singleton.fastq.gz"
-                                        : "out=${prefix}_1_repaired.fastq.gz out2=${prefix}_2_repaired.fastq.gz outs=${prefix}_singleton.fastq.gz"
+    prefix = task.ext.prefix ?: "${meta.id}"
     """
     echo "" | gzip > ${prefix}_1_repaired.fastq.gz
     echo "" | gzip > ${prefix}_2_repaired.fastq.gz

diff --git a/modules/nf-core/bbmap/repair/meta.yml b/modules/nf-core/bbmap/repair/meta.yml
@@ -9,8 +9,8 @@ tools:
   - repair:
       description: Repair.sh is a tool that re-pairs reads that became disordered or had some mates eliminated
         tools.
-      homepage: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
-      documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
+      homepage: https://jgi.doe.gov/data-and-tools/software-tools/bbtools/
+      documentation: https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/
       licence: ["UC-LBL license (see package)"]
       identifier: biotools:bbmap
 

diff --git a/modules/nf-core/bbmap/repair/tests/main.nf.test b/modules/nf-core/bbmap/repair/tests/main.nf.test
@@ -10,12 +10,14 @@ nextflow_process {
     tag "bbmap/repair"
 
     test("sarscov2_illumina_paired - fastq_gz") {
-
+        config "./nextflow.config"
 
         when {
+            params {
+                module_args = 'qin=33'
+            }
             process {
                 """
-
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
                     [file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
@@ -25,23 +27,23 @@ nextflow_process {
                 """
             }
         }
-
         then {
             assertAll(
                 { assert process.success },
                 { assert snapshot(process.out.versions).match() }
             )
         }
-
     }
 
     test("sarscov2_illumina_interleaved - fastq_gz") {
-
+        config "./nextflow.config"
 
         when {
+            params {
+                module_args = 'qin=33'
+            }
             process {
                 """
-
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
                     [file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true)]
@@ -50,24 +52,24 @@ nextflow_process {
                 """
             }
         }
-
         then {
             assertAll(
                 { assert process.success },
                 { assert snapshot(process.out.versions).match() }
             )
         }
-
     }
 
     test("sarscov2_illumina_paired - fastq_gz - stub") {
-
+        config "./nextflow.config"
         options "-stub"
 
         when {
+            params {
+                module_args = 'qin=33'
+            }
             process {
                 """
-
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
                     [file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
@@ -77,24 +79,24 @@ nextflow_process {
                 """
             }
         }
-
         then {
             assertAll(
                 { assert process.success },
                 { assert snapshot(process.out).match() }
             )
         }
-
     }
 
     test("sarscov2_illumina_interleaved - fastq_gz - stub") {
-
+        config "./nextflow.config"
         options "-stub"
 
         when {
+            params {
+                module_args = 'qin=33'
+            }
             process {
                 """
-
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
                     [file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true)]
@@ -103,14 +105,11 @@ nextflow_process {
                 """
             }
         }
-
         then {
             assertAll(
                 { assert process.success },
                 { assert snapshot(process.out).match() }
             )
         }
-
     }
-
 }
diff --git a/modules/nf-core/bbmap/repair/tests/main.nf.test.snap b/modules/nf-core/bbmap/repair/tests/main.nf.test.snap
@@ -0,0 +1,156 @@
+{
+    "sarscov2_illumina_paired - fastq_gz": {
+        "content": [
+            [
+                "versions.yml:md5,006e8f2167df95a778b428413ed9d859"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-19T11:01:18.284624712"
+    },
+    "sarscov2_illumina_interleaved - fastq_gz - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_1_repaired.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_2_repaired.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_singleton.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,006e8f2167df95a778b428413ed9d859"
+                ],
+                "3": [
+                    "test.repair.sh.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "log": [
+                    "test.repair.sh.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "repaired": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_1_repaired.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_2_repaired.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "singleton": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_singleton.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,006e8f2167df95a778b428413ed9d859"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-19T11:02:01.385727451"
+    },
+    "sarscov2_illumina_interleaved - fastq_gz": {
+        "content": [
+            [
+                "versions.yml:md5,006e8f2167df95a778b428413ed9d859"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-19T11:01:32.752620818"
+    },
+    "sarscov2_illumina_paired - fastq_gz - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_1_repaired.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_2_repaired.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_singleton.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,006e8f2167df95a778b428413ed9d859"
+                ],
+                "3": [
+                    "test.repair.sh.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "log": [
+                    "test.repair.sh.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "repaired": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_1_repaired.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_2_repaired.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "singleton": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_singleton.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,006e8f2167df95a778b428413ed9d859"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-19T11:01:47.341193946"
+    }
+}
diff --git a/modules/nf-core/bbmap/repair/tests/nextflow.config b/modules/nf-core/bbmap/repair/tests/nextflow.config
@@ -0,0 +1,6 @@
+process {
+    withName: BBMAP_REPAIR {
+        ext.args = params.module_args
+        cpus     = { 2 * task.attempt }
+    }
+}