fix calder version

modules/nf-core/calder2/main.nf

@@ -2,21 +2,20 @@ process CALDER2 {
     tag "$meta.id"
     label 'process_high'
 
-    // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/r-calder2:0.7--r43hdfd78af_1' :
         'biocontainers/r-calder2:0.7--r43hdfd78af_1' }"
 
-
     input:
     tuple val(meta), path(cool)
     val resolution
 
     output:
-    tuple val(meta), path("${prefix}/")                     , emit: output_folder
-    tuple val(meta), path("${prefix}/intermediate_data/")   , emit: intermediate_data_folder      , optional: true
-    path "versions.yml"                                     , emit: versions
+    tuple val(meta), path("${prefix}/")                    , emit: output_folder
+    tuple val(meta), path("${prefix}/intermediate_data/")  , emit: intermediate_data_folder, optional: true
+    // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    tuple val("${task.process}"), val('calder'), val('0.7'), emit: versions_calder, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -26,7 +25,6 @@ process CALDER2 {
     prefix = task.ext.prefix ?: "${meta.id}"
     def suffix = resolution ? "::/resolutions/$resolution" : ""
     def cpus = task.cpus ?: 1
-    def VERSION = '0.7' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     # getting binsize as mandatory input for calder
     binsize="\$(cooler info --field bin-size $cool$suffix)"
@@ -37,16 +35,10 @@ process CALDER2 {
         --type cool \\
         --bin_size "\${binsize}" \\
         $args
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        calder: $VERSION
-    END_VERSIONS
     """
 
     stub:
     prefix = task.ext.prefix ?: "${meta.id}"
-    def VERSION = '0.7' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     mkdir -p ${prefix}/sub_compartments
     mkdir -p ${prefix}/sub_domains
@@ -58,10 +50,5 @@ process CALDER2 {
     touch ${prefix}/sub_compartments/cor_with_ref.txt
 
     touch ${prefix}/sub_domains/all_nested_boundaries.bed
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        calder: $VERSION
-    END_VERSIONS
     """
 }

modules/nf-core/calder2/meta.yml

@@ -14,48 +14,63 @@ tools:
       documentation: "https://github.com/CSOgroup/CALDER2"
       tool_dev_url: "https://github.com/CSOgroup/CALDER2"
       doi: "10.1038/s41467-021-22666-3"
-      licence: ["MIT"]
+      licence:
+        - "MIT"
       identifier: ""
 input:
   - - meta:
         type: map
-        description: Groovy Map containing sample information. E.g. [ id:'test', single_end:false
-          ]
+        description: Groovy Map containing sample information. E.g. [ id:'test',
+          single_end:false ]
     - cool:
         type: file
         description: Path to COOL file
         pattern: "*.{cool.mcool}"
         ontologies: []
   - resolution:
       type: integer
-      description: In case a .mcool file is provided, which resolution level to use
-        for the analysis
+      description: In case a .mcool file is provided, which resolution level to
+        use for the analysis
 output:
   output_folder:
     - - meta:
           type: map
-          description: Groovy Map containing sample information. E.g. [ id:'test', single_end:false
-            ]
+          description: Groovy Map containing sample information. E.g. [ id:'test',
+            single_end:false ]
       - ${prefix}/:
           type: directory
-          description: Output folder containing sub-compartment (.tsv/.bed) and domain
-            boundaries calls (.bed)
+          description: Output folder containing sub-compartment (.tsv/.bed) and
+            domain boundaries calls (.bed)
   intermediate_data_folder:
     - - meta:
           type: map
-          description: Groovy Map containing sample information. E.g. [ id:'test', single_end:false
-            ]
+          description: Groovy Map containing sample information. E.g. [ id:'test',
+            single_end:false ]
       - ${prefix}/intermediate_data/:
           type: directory
-          description: Output folder containing intermediate data produced during the
-            computation
+          description: Output folder containing intermediate data produced during
+            the computation
+  versions_calder:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - calder:
+          type: string
+          description: The name of the tool
+      - "0.7":
+          type: string
+          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
+      - calder:
+          type: string
+          description: The name of the tool
+      - "0.7":
+          type: string
+          description: The expression to obtain the version of the tool
 authors:
   - "@lucananni93"
 maintainers:

modules/nf-core/calder2/tests/main.nf.test

@@ -1,5 +1,3 @@
-import groovy.io.FileType
-
 nextflow_process {
 
     name "Test Process CALDER2"
@@ -14,15 +12,17 @@ nextflow_process {
     test("test-calder2-cool") {
 
         when {
+            params {
+                module_args = '--genome hg38'
+            }
             process {
                 """
                 input[0] = [
-                    [ id:'test' ], //meta map
+                    [ id:'test' ],
 				    file('https://raw.githubusercontent.com/CSOgroup/CALDER2/main/tests/testthat/data/test.cool', checkIfExists: true)
                 ]
 
 				input[1] = [:]
-
                 """
             }
         }
@@ -31,12 +31,9 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 {
+                    def output_dir = file(process.out.output_folder[0][1])
                     def all_files = []
-
-                    file(process.out.output_folder[0][1]).eachFileRecurse (FileType.FILES) { file ->
-                        all_files << file
-                    }
-
+                    output_dir.eachFileRecurse { all_files << it }
                     def all_file_names = all_files.collect { it.name }.toSorted()
 
                     def stable_file_names = [
@@ -52,7 +49,7 @@ nextflow_process {
                     assert snapshot(
                         all_file_names,
                         stable_files,
-                        process.out.versions[0]
+                        process.out.findAll { key, val -> key.startsWith('versions') }
                     ).match()
                 }
             )
@@ -62,15 +59,17 @@ nextflow_process {
     test("test-calder2-mcool") {
 
         when {
+            params {
+                module_args = '--genome hg38'
+            }
             process {
                 """
                 input[0] = [
-                    [ id:'test' ], //meta map
+                    [ id:'test' ],
 				    file('https://raw.githubusercontent.com/CSOgroup/CALDER2/main/tests/testthat/data/test.mcool', checkIfExists: true)
                 ]
 
                 input[1] = 100000
-
                 """
             }
         }
@@ -79,12 +78,9 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 {
+                    def output_dir = file(process.out.output_folder[0][1])
                     def all_files = []
-
-                    file(process.out.output_folder[0][1]).eachFileRecurse (FileType.FILES) { file ->
-                        all_files << file
-                    }
-
+                    output_dir.eachFileRecurse { all_files << it }
                     def all_file_names = all_files.collect { it.name }.toSorted()
 
                     def stable_file_names = [
@@ -100,7 +96,7 @@ nextflow_process {
                     assert snapshot(
                         all_file_names,
                         stable_files,
-                        process.out.versions[0]
+                        process.out.findAll { key, val -> key.startsWith('versions') }
                     ).match()
                 }
             )
@@ -111,23 +107,25 @@ nextflow_process {
         options '-stub'
 
         when {
+            params {
+                module_args = '--genome hg38'
+            }
             process {
                 """
                 input[0] = [
-                    [ id:'test' ], //meta map
+                    [ id:'test' ],
 				    file('https://raw.githubusercontent.com/CSOgroup/CALDER2/main/tests/testthat/data/test.mcool', checkIfExists: true)
                 ]
 
                 input[1] = 100000
-
                 """
             }
         }
 
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
     }