feat: Use newest software version handler

modules.json

@@ -33,6 +33,12 @@
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/checkm/lineagewf/checkm-lineagewf.diff"
                     },
+                    "custom/dumpsoftwareversions": {
+                        "branch": "master",
+                        "git_sha": "05c280924b6c768d484c7c443dad5e605c4ff4b4",
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff"
+                    },
                     "diamond/blastp": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",

modules/local/rgi.nf

@@ -11,19 +11,25 @@ process UPDATE_RGI_DB {
 
     output:
     path "card.json", emit: card_json
-    path "card.version.txt", emit: card_version
+    path "versions.yml", emit: card_version
 
     script:
     """
     curl https://card.mcmaster.ca/latest/data --output card.tar.bz2
     tar xvf card.tar.bz2
-    python -c "import json;fh = open('card.json');card=json.load(fh);print(card['_version'])" > card.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        card: \$(echo \$(python -c "import json;fh = open('card.json');card=json.load(fh);print(card['_version'])"))
+    END_VERSIONS
     """
 
     stub:
     """
     touch card.json
-    touch card.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        card: 1.0
+    END_VERSIONS
     """
 }
 
@@ -48,7 +54,7 @@ process RGI {
 
     output:
     tuple val(meta), path("${meta.id}_rgi.txt"), emit: tsv
-    path "*.version.txt", emit: version
+    path "versions.yml", emit: version
 
     script:
     def software = getSoftwareName(task.process)
@@ -58,13 +64,19 @@ process RGI {
     rgi load -i $card_db --local
     rgi main --local --input_sequence $fasta --output_file ${meta.id}_rgi --input_type contig --clean --include_loose
 
-    echo \$(rgi main --version 2>&1) > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        rgi: \$(echo \$(rgi main --version 2>&1))
+    END_VERSIONS
     """
     stub:
     def software = getSoftwareName(task.process)
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     """
     touch ${prefix}_rgi.txt
-    echo \$(rgi main --version 2>&1) > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        rgi: \$(echo \$(rgi main --version 2>&1))
+    END_VERSIONS
     """
 }

modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff

@@ -0,0 +1,18 @@
+Changes in module 'nf-core/custom/dumpsoftwareversions'
+--- modules/nf-core/custom/dumpsoftwareversions/main.nf
++++ modules/nf-core/custom/dumpsoftwareversions/main.nf
+@@ -2,10 +2,10 @@
+     label 'process_single'
+
+     // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container
+-    conda "bioconda::multiqc=1.15"
++    conda (params.enable_conda ? "bioconda::multiqc=1.15" : null)
+     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+         'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' :
+-        'biocontainers/multiqc:1.15--pyhdfd78af_0' }"
++        'quay.io/biocontainers/multiqc:1.15--pyhdfd78af_0' }"
+
+     input:
+     path versions
+
+************************************************************

modules/nf-core/custom/dumpsoftwareversions/main.nf

@@ -0,0 +1,24 @@
+process CUSTOM_DUMPSOFTWAREVERSIONS {
+    label 'process_single'
+
+    // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container
+    conda (params.enable_conda ? "bioconda::multiqc=1.15" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' :
+        'quay.io/biocontainers/multiqc:1.15--pyhdfd78af_0' }"
+
+    input:
+    path versions
+
+    output:
+    path "software_versions.yml"    , emit: yml
+    path "software_versions_mqc.yml", emit: mqc_yml
+    path "versions.yml"             , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    template 'dumpsoftwareversions.py'
+}

modules/nf-core/custom/dumpsoftwareversions/meta.yml

@@ -0,0 +1,36 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
+name: custom_dumpsoftwareversions
+description: Custom module used to dump software versions within the nf-core pipeline template
+keywords:
+  - custom
+  - dump
+  - version
+tools:
+  - custom:
+      description: Custom module used to dump software versions within the nf-core pipeline template
+      homepage: https://github.com/nf-core/tools
+      documentation: https://github.com/nf-core/tools
+      licence: ["MIT"]
+input:
+  - versions:
+      type: file
+      description: YML file containing software versions
+      pattern: "*.yml"
+
+output:
+  - yml:
+      type: file
+      description: Standard YML file containing software versions
+      pattern: "software_versions.yml"
+  - mqc_yml:
+      type: file
+      description: MultiQC custom content YML file containing software versions
+      pattern: "software_versions_mqc.yml"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@drpatelh"
+  - "@grst"

modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py

@@ -0,0 +1,101 @@
+#!/usr/bin/env python
+
+
+"""Provide functions to merge multiple versions.yml files."""
+
+
+import yaml
+import platform
+from textwrap import dedent
+
+
+def _make_versions_html(versions):
+    """Generate a tabular HTML output of all versions for MultiQC."""
+    html = [
+        dedent(
+            """\\
+            <style>
+            #nf-core-versions tbody:nth-child(even) {
+                background-color: #f2f2f2;
+            }
+            </style>
+            <table class="table" style="width:100%" id="nf-core-versions">
+                <thead>
+                    <tr>
+                        <th> Process Name </th>
+                        <th> Software </th>
+                        <th> Version  </th>
+                    </tr>
+                </thead>
+            """
+        )
+    ]
+    for process, tmp_versions in sorted(versions.items()):
+        html.append("<tbody>")
+        for i, (tool, version) in enumerate(sorted(tmp_versions.items())):
+            html.append(
+                dedent(
+                    f"""\\
+                    <tr>
+                        <td><samp>{process if (i == 0) else ''}</samp></td>
+                        <td><samp>{tool}</samp></td>
+                        <td><samp>{version}</samp></td>
+                    </tr>
+                    """
+                )
+            )
+        html.append("</tbody>")
+    html.append("</table>")
+    return "\\n".join(html)
+
+
+def main():
+    """Load all version files and generate merged output."""
+    versions_this_module = {}
+    versions_this_module["${task.process}"] = {
+        "python": platform.python_version(),
+        "yaml": yaml.__version__,
+    }
+
+    with open("$versions") as f:
+        versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module
+
+    # aggregate versions by the module name (derived from fully-qualified process name)
+    versions_by_module = {}
+    for process, process_versions in versions_by_process.items():
+        module = process.split(":")[-1]
+        try:
+            if versions_by_module[module] != process_versions:
+                raise AssertionError(
+                    "We assume that software versions are the same between all modules. "
+                    "If you see this error-message it means you discovered an edge-case "
+                    "and should open an issue in nf-core/tools. "
+                )
+        except KeyError:
+            versions_by_module[module] = process_versions
+
+    versions_by_module["Workflow"] = {
+        "Nextflow": "$workflow.nextflow.version",
+        "$workflow.manifest.name": "$workflow.manifest.version",
+    }
+
+    versions_mqc = {
+        "id": "software_versions",
+        "section_name": "${workflow.manifest.name} Software Versions",
+        "section_href": "https://github.com/${workflow.manifest.name}",
+        "plot_type": "html",
+        "description": "are collected at run time from the software output.",
+        "data": _make_versions_html(versions_by_module),
+    }
+
+    with open("software_versions.yml", "w") as f:
+        yaml.dump(versions_by_module, f, default_flow_style=False)
+    with open("software_versions_mqc.yml", "w") as f:
+        yaml.dump(versions_mqc, f, default_flow_style=False)
+
+    with open("versions.yml", "w") as f:
+        yaml.dump(versions_this_module, f, default_flow_style=False)
+
+
+if __name__ == "__main__":
+    main()