diff --git a/modules/nf-core/calder2/main.nf b/modules/nf-core/calder2/main.nf index d2300f591c5d..131a331da9ec 100644 --- a/modules/nf-core/calder2/main.nf +++ b/modules/nf-core/calder2/main.nf @@ -16,7 +16,8 @@ process CALDER2 { 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("${task.process}"), val('calder'), val('0.7'), emit: versions_calder, topic: versions + // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. when: task.ext.when == null || task.ext.when @@ -26,7 +27,6 @@ process CALDER2 { prefix = task.ext.prefix ?: "${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 +37,10 @@ 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 +52,5 @@ 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 """ } diff --git a/modules/nf-core/calder2/meta.yml b/modules/nf-core/calder2/meta.yml index 9e353380279b..73eb35a20db1 100644 --- a/modules/nf-core/calder2/meta.yml +++ b/modules/nf-core/calder2/meta.yml @@ -14,13 +14,14 @@ 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 @@ -28,34 +29,48 @@ input: 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: diff --git a/modules/nf-core/calder2/tests/main.nf.test b/modules/nf-core/calder2/tests/main.nf.test index 7833470e7827..71f4fb441aa9 100644 --- a/modules/nf-core/calder2/tests/main.nf.test +++ b/modules/nf-core/calder2/tests/main.nf.test @@ -52,7 +52,7 @@ nextflow_process { assert snapshot( all_file_names, stable_files, - process.out.versions[0] + process.out.versions_calder[0] ).match() } ) @@ -100,7 +100,7 @@ nextflow_process { assert snapshot( all_file_names, stable_files, - process.out.versions[0] + process.out.versions_calder[0] ).match() } ) diff --git a/modules/nf-core/calder2/tests/main.nf.test.snap b/modules/nf-core/calder2/tests/main.nf.test.snap index 22312cd21764..e02680f09967 100644 --- a/modules/nf-core/calder2/tests/main.nf.test.snap +++ b/modules/nf-core/calder2/tests/main.nf.test.snap @@ -25,7 +25,11 @@ ], "2": [ - "versions.yml:md5,b312ffd67c18a79a5db11b78777c00d0" + [ + "CALDER2", + "calder", + "0.7" + ] ], "intermediate_data_folder": [ @@ -49,16 +53,20 @@ ] ] ], - "versions": [ - "versions.yml:md5,b312ffd67c18a79a5db11b78777c00d0" + "versions_calder": [ + [ + "CALDER2", + "calder", + "0.7" + ] ] } ], + "timestamp": "2026-03-13T10:44:04.45799756", "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-09-02T15:17:11.435944" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "test-calder2-cool": { "content": [ @@ -77,13 +85,20 @@ "cor_with_ref.txt:md5,54f954d92df161db5cae7845d2786ad2", "all_nested_boundaries.bed:md5,56172ee755f573ad57320273ca0f52cd" ], - "versions.yml:md5,b312ffd67c18a79a5db11b78777c00d0" + [ + "CALDER2", + "calder", + "0.7" + ] ], + "timestamp": "2026-03-13T10:24:39.4710294", "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.4", + "nextflow": "25.10.4" }, - "timestamp": "2024-09-02T15:16:37.504391" + "versions_calder": [ + ["CALDER2", "calder", "0.7"] + ] }, "test-calder2-mcool": { "content": [ @@ -102,12 +117,19 @@ "cor_with_ref.txt:md5,f748876d367d0fdb751bd00e8e9bf60a", "all_nested_boundaries.bed:md5,c066de5e2e789e3fe65b900a3b0a4876" ], - "versions.yml:md5,b312ffd67c18a79a5db11b78777c00d0" + [ + "CALDER2", + "calder", + "0.7" + ] ], + "timestamp": "2026-03-13T10:26:07.222064175", "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.4", + "nextflow": "25.10.4" }, - "timestamp": "2024-09-02T15:17:06.081233" + "versions_calder": [ + ["CALDER2", "calder", "0.7"] + ] } } \ No newline at end of file diff --git a/modules/nf-core/calder2/tests/nextflow.config b/modules/nf-core/calder2/tests/nextflow.config index 7bc72018f58b..45b1c2008460 100644 --- a/modules/nf-core/calder2/tests/nextflow.config +++ b/modules/nf-core/calder2/tests/nextflow.config @@ -1,3 +1,7 @@ process { ext.args = '--genome hg38' } +singularity { + enabled = true + pullTimeout = '1h' +}