Bump version cat/cat to pigz 2.8 & rewrite nf-test & topic channel

modules/nf-core/cat/cat/environment.yml

@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - conda-forge::pigz=2.3.4
+  - conda-forge::pigz=2.8

modules/nf-core/cat/cat/main.nf

@@ -4,15 +4,15 @@ process CAT_CAT {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pigz:2.3.4' :
-        'biocontainers/pigz:2.3.4' }"
+        'https://depot.galaxyproject.org/singularity/pigz:2.8' :
+        'biocontainers/pigz:2.8' }"
 
     input:
     tuple val(meta), path(files_in)
 
     output:
     tuple val(meta), path("${prefix}"), emit: file_out
-    path "versions.yml"               , emit: versions
+    tuple val("${task.process}"), val("pigz"), eval("pigz --version 2>&1 | sed 's/pigz //g'"),  topic: versions, emit: versions_cat
 
     when:
     task.ext.when == null || task.ext.when

modules/nf-core/cat/cat/meta.yml

@@ -28,16 +28,33 @@ output:
           description: Groovy Map containing sample information
       - ${prefix}:
           type: file
-          description: Concatenated file. Will be gzipped if file_out ends with ".gz"
+          description: Concatenated file. Will be gzipped if file_out ends with
+            ".gz"
           pattern: "${file_out}"
           ontologies: []
+  versions_cat:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - pigz:
+          type: string
+          description: The name of the tool
+      - "pigz --version 2>&1 | sed 's/pigz //g'":
+          type: eval
+          description: The expression to obtain the version of the tool
+
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - pigz:
+          type: string
+          description: The name of the tool
+      - "pigz --version 2>&1 | sed 's/pigz //g'":
+          type: eval
+          description: The expression to obtain the version of the tool
+
 authors:
   - "@erikrikarddaniel"
   - "@FriederikeHanssen"

modules/nf-core/cat/cat/tests/main.nf.test

@@ -3,16 +3,14 @@ nextflow_process {
     name "Test Process CAT_CAT"
     script "../main.nf"
     process "CAT_CAT"
+
     tag "modules"
     tag "modules_nfcore"
     tag "cat"
     tag "cat/cat"
 
-    test("test_cat_name_conflict") {
+    test("sarscov2 - genome - error: name conflict") {
         when {
-            params {
-                outdir   = "${outputDir}"
-            }
             process {
                 """
                 input[0] =
@@ -30,16 +28,13 @@ nextflow_process {
             assertAll(
                 { assert !process.success },
                 { assert process.stdout.toString().contains("The name of the input file can't be the same as for the output prefix") },
-                { assert snapshot(process.out.versions).match() }
+                { assert snapshot(process.out).match() }
             )
         }
     }
 
-    test("test_cat_unzipped_unzipped") {
+    test("sarscov2 - [ fasta, sizes ] - unzipped") {
         when {
-            params {
-                outdir   = "${outputDir}"
-            }
             process {
                 """
                 input[0] =
@@ -62,11 +57,8 @@ nextflow_process {
     }
 
 
-    test("test_cat_zipped_zipped") {
+    test("sarscov2 - [ gff3_gz, maf_gz ] - zipped") {
         when {
-            params {
-                outdir   = "${outputDir}"
-            }
             process {
                 """
                 input[0] =
@@ -81,25 +73,20 @@ nextflow_process {
             }
         }
         then {
-            def lines = path(process.out.file_out.get(0).get(1)).linesGzip
             assertAll(
                 { assert process.success },
-                { assert snapshot(
-                    lines[0..5],
-                    lines.size(),
-                    process.out.versions
-                    ).match()
+                { assert snapshot(process.out).match()
                 }
             )
         }
     }
 
-    test("test_cat_zipped_unzipped") {
-        config './nextflow_zipped_unzipped.config'
+    test("sarscov2 - [ gff3_gz, maf_gz ] - unzipped") {
+        config './nextflow.config'
 
         when {
             params {
-                outdir   = "${outputDir}"
+                cat_prefix = "cat.txt"
             }
             process {
                 """
@@ -124,11 +111,12 @@ nextflow_process {
 
     }
 
-    test("test_cat_unzipped_zipped") {
-        config './nextflow_unzipped_zipped.config'
+    test("sarscov2 - [ fasta, sizes ] - zipped") {
+        config './nextflow.config'
+
         when {
             params {
-                outdir   = "${outputDir}"
+                cat_prefix = "cat.txt.gz"
             }
             process {
                 """
@@ -144,24 +132,19 @@ nextflow_process {
             }
         }
         then {
-            def lines = path(process.out.file_out.get(0).get(1)).linesGzip
             assertAll(
                 { assert process.success },
-                { assert snapshot(
-                    lines[0..5],
-                    lines.size(),
-                    process.out.versions
-                    ).match()
-                }
+                { assert snapshot(process.out).match() }
             )
         }
     }
 
-    test("test_cat_one_file_unzipped_zipped") {
-        config './nextflow_unzipped_zipped.config'
+    test("sarscov2 - fasta - zipped") {
+        config './nextflow.config'
+
         when {
             params {
-                outdir   = "${outputDir}"
+                cat_prefix = "cat.txt.gz"
             }
             process {
                 """
@@ -176,15 +159,33 @@ nextflow_process {
             }
         }
         then {
-            def lines = path(process.out.file_out.get(0).get(1)).linesGzip
             assertAll(
                 { assert process.success },
-                { assert snapshot(
-                    lines[0..5],
-                    lines.size(),
-                    process.out.versions
-                    ).match()
-                }
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 - fasta - unzipped - stub") {
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] =
+                    [
+                        [ id:'test', single_end:true ],
+                        [
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                        ]
+                    ]
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
             )
         }
     }