Dp24 windowmasker (nf-core#4924)

* Adding updated modules and nf-tests * Remove pytest folders and edut the pytest file * reverting convert to 2.14 * reverting convert to 2.15 * Forgot the conda environmrnt
RSC-RP · Mar 20, 2024 · e982959 · e982959
1 parent 8e78842
commit e982959
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Showing 30 changed files with 520 additions and 184 deletions.
diff --git a/modules/nf-core/windowmasker/convert/environment.yml b/modules/nf-core/windowmasker/convert/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::blast=2.13.0
+  - bioconda::blast=2.15.0
diff --git a/modules/nf-core/windowmasker/convert/main.nf b/modules/nf-core/windowmasker/convert/main.nf
@@ -4,8 +4,8 @@ process WINDOWMASKER_CONVERT {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/blast:2.13.0--hf3cf87c_0':
-        'biocontainers/blast:2.13.0--hf3cf87c_0' }"
+        'https://depot.galaxyproject.org/singularity/blast:2.15.0--pl5321h6f7f691_1':
+        'biocontainers/blast:2.15.0--pl5321h6f7f691_1' }"
 
     input:
     tuple val(meta), path(counts)
@@ -18,11 +18,11 @@ process WINDOWMASKER_CONVERT {
     task.ext.when == null || task.ext.when
 
     script:
-    def args   = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    def outfmt =    args.contains('-sformat binary')  ? 'binary'  :
-                    args.contains('-sformat oascii')  ? 'oascii'  :
-                    args.contains('-sformat obinary') ? 'obinary' :
+    def args   =    task.ext.args                       ?: ''
+    def prefix =    task.ext.prefix                     ?: "${meta.id}"
+    def outfmt =    args.contains('-sformat binary')    ? 'binary'  :
+                    args.contains('-sformat oascii')    ? 'oascii'  :
+                    args.contains('-sformat obinary')   ? 'obinary' :
                     'ascii'
     output  = "${prefix}.${outfmt}"
     """
@@ -38,11 +38,11 @@ process WINDOWMASKER_CONVERT {
     """
 
     stub:
-    def args   = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    def outfmt =    args.contains('-sformat binary')  ? 'binary'  :
-                    args.contains('-sformat oascii')  ? 'oascii'  :
-                    args.contains('-sformat obinary') ? 'obinary' :
+    def args   =    task.ext.args                       ?: ''
+    def prefix =    task.ext.prefix                     ?: "${meta.id}"
+    def outfmt =    args.contains('-sformat binary')    ? 'binary'  :
+                    args.contains('-sformat oascii')    ? 'oascii'  :
+                    args.contains('-sformat obinary')   ? 'obinary' :
                     'ascii'
     output  = "${prefix}.${outfmt}"
     """

diff --git a/modules/nf-core/windowmasker/convert/tests/convert_binary.config b/modules/nf-core/windowmasker/convert/tests/convert_binary.config
@@ -0,0 +1,5 @@
+process {
+    withName: WINDOWMASKER_CONVERT {
+        ext.args = '-sformat binary'
+    }
+}
diff --git a/modules/nf-core/windowmasker/convert/tests/convert_oascii.config b/modules/nf-core/windowmasker/convert/tests/convert_oascii.config
@@ -0,0 +1,5 @@
+process {
+    withName: WINDOWMASKER_CONVERT {
+        ext.args = '-sformat oascii'
+    }
+}
diff --git a/modules/nf-core/windowmasker/convert/tests/convert_obinary.config b/modules/nf-core/windowmasker/convert/tests/convert_obinary.config
@@ -0,0 +1,5 @@
+process {
+    withName: WINDOWMASKER_CONVERT {
+        ext.args = '-sformat obinary'
+    }
+}
diff --git a/modules/nf-core/windowmasker/convert/tests/main.nf.test b/modules/nf-core/windowmasker/convert/tests/main.nf.test
@@ -0,0 +1,105 @@
+nextflow_process {
+
+    name "Test Process WINDOWMASKER_CONVERT"
+    script "../main.nf"
+    process "WINDOWMASKER_CONVERT"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "windowmasker"
+    tag "windowmasker/convert"
+    tag "windowmasker/mkcounts"
+
+    setup {
+        run("WINDOWMASKER_MKCOUNTS") {
+            script "../../mkcounts/main.nf"
+            process {
+                """
+                input[0] = [
+                    [id: "test" ],
+                    [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)]
+                ]
+                """
+            }
+        }
+    }
+
+    test("sarscov2_fasta_binary") {
+        config "./convert_binary.config"
+        when {
+            process {
+                """
+                input[0] = WINDOWMASKER_MKCOUNTS.out.counts
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2_fasta_obinary") {
+        config "./convert_obinary.config"
+        when {
+            process {
+                """
+                input[0] = WINDOWMASKER_MKCOUNTS.out.counts
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2_fasta_oascii") {
+        config "./convert_oascii.config"
+        when {
+            process {
+                """
+                input[0] = WINDOWMASKER_MKCOUNTS.out.counts
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2_fasta_stub") {
+
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [id: "test" ],
+                    [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)]
+                ]
+                """
+            }
+        }
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/windowmasker/convert/tests/main.nf.test.snap b/modules/nf-core/windowmasker/convert/tests/main.nf.test.snap
diff --git a/modules/nf-core/windowmasker/convert/tests/tags.yml b/modules/nf-core/windowmasker/convert/tests/tags.yml
@@ -0,0 +1,2 @@
+windowmasker/convert:
+  - "modules/nf-core/windowmasker/convert/**"
diff --git a/modules/nf-core/windowmasker/mkcounts/environment.yml b/modules/nf-core/windowmasker/mkcounts/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::blast=2.14.0
+  - bioconda::blast=2.15.0
diff --git a/modules/nf-core/windowmasker/mkcounts/main.nf b/modules/nf-core/windowmasker/mkcounts/main.nf
@@ -4,8 +4,8 @@ process WINDOWMASKER_MKCOUNTS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/blast:2.14.0--h7d5a4b4_1':
-        'biocontainers/blast:2.14.0--h7d5a4b4_1' }"
+        'https://depot.galaxyproject.org/singularity/blast:2.15.0--pl5321h6f7f691_1':
+        'biocontainers/blast:2.15.0--pl5321h6f7f691_1' }"
 
     input:
     tuple val(meta), path(ref)
@@ -21,11 +21,11 @@ process WINDOWMASKER_MKCOUNTS {
     def args    = task.ext.args     ?: ""
     def prefix  = task.ext.prefix   ?: "${meta.id}"
 
-    def memory = 3072
+    def memory  = 3072
     if (!task.memory) {
         log.info '[WINDOWMASKER: MK_COUNTS] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
     } else {
-        memory = (task.memory.toMega()).intValue()
+        memory  = (task.memory.toMega()).intValue()
     }
 
     """

diff --git a/modules/nf-core/windowmasker/mkcounts/tests/main.nf.test b/modules/nf-core/windowmasker/mkcounts/tests/main.nf.test
@@ -0,0 +1,59 @@
+nextflow_process {
+
+    name "Test Process WINDOWMASKER_MKCOUNTS"
+    script "../main.nf"
+    process "WINDOWMASKER_MKCOUNTS"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "windowmasker"
+    tag "windowmasker/mkcounts"
+
+    test("sarscov2_fasta") {
+
+        when {
+            params {
+                // define parameters here. Example:
+                // outdir = "tests/results"
+            }
+            process {
+                """
+                input[0] = [
+                    [id: "test" ],
+                    [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)]
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+    test("sarscov2_fasta_stub") {
+
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [id: "test" ],
+                    [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)]
+                ]
+                """
+            }
+        }
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		windowmasker/convert:
		- "modules/nf-core/windowmasker/convert/**"