Merge pull request #1951 from SamStudio8/workflowmain-version

Add --version to NfCoreTemplate
nf-core · Nov 18, 2022 · 3ed5f29 · 3ed5f29
2 parents 78ede41 + 960e5cf
commit 3ed5f29
Show file tree

Hide file tree

Showing 7 changed files with 40 additions and 7 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,6 +7,7 @@
 - Fix lint warnings for `samplesheet_check.nf` module
 - Add codespaces template ([#1957](https://github.com/nf-core/tools/pull/1957))
 - Check that the workflow name provided with a template doesn't contain dashes ([#1822](https://github.com/nf-core/tools/pull/1822))
+- `nextflow run <pipeline> --version` will now print the workflow version from the manifest and exit ([#1951](https://github.com/nf-core/tools/pull/1951))
 
 ### Linting
 

diff --git a/nf_core/lint/nextflow_config.py b/nf_core/lint/nextflow_config.py
@@ -141,7 +141,6 @@ def nextflow_config(self):
     ]
     # Old depreciated vars - fail if present
     config_fail_ifdefined = [
-        "params.version",
         "params.nf_required_version",
         "params.container",
         "params.singleEnd",

diff --git a/nf_core/pipeline-template/lib/NfcoreSchema.groovy b/nf_core/pipeline-template/lib/NfcoreSchema.groovy
@@ -46,7 +46,6 @@ class NfcoreSchema {
             'quiet',
             'syslog',
             'v',
-            'version',
 
             // Options for `nextflow run` command
             'ansi',

diff --git a/nf_core/pipeline-template/lib/NfcoreTemplate.groovy b/nf_core/pipeline-template/lib/NfcoreTemplate.groovy
@@ -32,6 +32,25 @@ class NfcoreTemplate {
         }
     }
 
+    //
+    // Generate version string
+    //
+    public static String version(workflow) {
+        String version_string = ""
+
+        if (workflow.manifest.version) {
+            def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
+            version_string += "${prefix_v}${workflow.manifest.version}"
+        }
+
+        if (workflow.commitId) {
+            def git_shortsha = workflow.commitId.substring(0, 7)
+            version_string += "-g${git_shortsha}"
+        }
+
+        return version_string
+    }
+
     //
     // Construct and send completion email
     //
@@ -61,7 +80,7 @@ class NfcoreTemplate {
         misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp
 
         def email_fields = [:]
-        email_fields['version']      = workflow.manifest.version
+        email_fields['version']      = NfcoreTemplate.version(workflow)
         email_fields['runName']      = workflow.runName
         email_fields['success']      = workflow.success
         email_fields['dateComplete'] = workflow.complete
@@ -170,7 +189,7 @@ class NfcoreTemplate {
         misc_fields['nxf_timestamp']                        = workflow.nextflow.timestamp
 
         def msg_fields = [:]
-        msg_fields['version']      = workflow.manifest.version
+        msg_fields['version']      = NfcoreTemplate.version(workflow)
         msg_fields['runName']      = workflow.runName
         msg_fields['success']      = workflow.success
         msg_fields['dateComplete'] = workflow.complete
@@ -300,6 +319,7 @@ class NfcoreTemplate {
     //
     public static String logo(workflow, monochrome_logs) {
         Map colors = logColours(monochrome_logs)
+        String workflow_version = NfcoreTemplate.version(workflow)
         String.format(
             """\n
             ${dashedLine(monochrome_logs)}{% if branded %}
@@ -308,7 +328,7 @@ class NfcoreTemplate {
             ${colors.blue}  |\\ | |__  __ /  ` /  \\ |__) |__         ${colors.yellow}}  {${colors.reset}
             ${colors.blue}  | \\| |       \\__, \\__/ |  \\ |___     ${colors.green}\\`-._,-`-,${colors.reset}
                                                     ${colors.green}`._,._,\'${colors.reset}{% endif %}
-            ${colors.purple}  ${workflow.manifest.name} v${workflow.manifest.version}${colors.reset}
+            ${colors.purple}  ${workflow.manifest.name} ${workflow_version}${colors.reset}
             ${dashedLine(monochrome_logs)}
             """.stripIndent()
         )

diff --git a/nf_core/pipeline-template/lib/WorkflowMain.groovy b/nf_core/pipeline-template/lib/WorkflowMain.groovy
@@ -19,7 +19,7 @@ class WorkflowMain {
     }
 
     //
-    // Print help to screen if required
+    // Generate help string
     //
     public static String help(workflow, params, log) {
         {% if igenomes -%}
@@ -36,7 +36,7 @@ class WorkflowMain {
     }
 
     //
-    // Print parameter summary log to screen
+    // Generate parameter summary log string
     //
     public static String paramsSummaryLog(workflow, params, log) {
         def summary_log = ''
@@ -57,6 +57,13 @@ class WorkflowMain {
             System.exit(0)
         }
 
+        // Print workflow version and exit on --version
+        if (params.version) {
+            String workflow_version = NfcoreTemplate.version(workflow)
+            log.info "${workflow.manifest.name} ${workflow_version}"
+            System.exit(0)
+        }
+
         // Validate workflow parameters via the JSON schema
         if (params.validate_params) {
             NfcoreSchema.validateParameters(workflow, params, log)

diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
@@ -37,6 +37,7 @@ params {
     monochrome_logs            = false
     hook_url                   = null
     help                       = false
+    version                    = false
     validate_params            = true
     show_hidden_params         = false
     schema_ignore_params       = 'genomes'

diff --git a/nf_core/pipeline-template/nextflow_schema.json b/nf_core/pipeline-template/nextflow_schema.json
@@ -176,6 +176,12 @@
                     "fa_icon": "fas fa-question-circle",
                     "hidden": true
                 },
+                "version": {
+                    "type": "boolean",
+                    "description": "Display version and exit.",
+                    "fa_icon": "fas fa-question-circle",
+                    "hidden": true
+                },
                 "publish_dir_mode": {
                     "type": "string",
                     "default": "copy",