Merge branch 'dev' into fix-970

CHANGELOG.md

@@ -2,14 +2,18 @@
 
 ## 1.14dev
 
-* Fixed an issue in the pipeline template regarding explicit disabling of unused container engines [[#972](https://github.com/nf-core/tools/pull/972)]
-* Fix overly strict `--max_time` formatting regex in template schema [[#973](https://github.com/nf-core/tools/issues/973)]
-* Try to fix the fix for the automated sync when we submit too many PRs at once [[#970](https://github.com/nf-core/tools/issues/970)]
+### Tools
+
 * Strip values from `nf-core launch` web response which are False and have no default in the schema [[#976](https://github.com/nf-core/tools/issues/976)]
+* Try to fix the fix for the automated sync when we submit too many PRs at once [[#970](https://github.com/nf-core/tools/issues/970)]
 
 ### Template
 
+* Fixed an issue regarding explicit disabling of unused container engines [[#972](https://github.com/nf-core/tools/pull/972)]
 * Removed trailing slash from `params.igenomes_base` to yield valid s3 paths (previous paths work with Nextflow but not aws cli)
+* Added a timestamp to the trace + timetime + report + dag filenames to fix overwrite issue on AWS
+* Rewrite the `params_summary_log()` function to properly ignore unset params and have nicer formatting [[#971](https://github.com/nf-core/tools/issues/971)]
+* Fix overly strict `--max_time` formatting regex in template schema [[#973](https://github.com/nf-core/tools/issues/973)]
 
 ## [v1.13.3 - Copper Crocodile Resurrection :crocodile:](https://github.com/nf-core/tools/releases/tag/1.13.2) - [2021-03-24]
 

nf_core/__main__.py

@@ -315,7 +315,10 @@ def lint(pipeline_dir, release, fix, show_passed, fail_ignored, markdown, json):
 
     Runs a large number of automated tests to ensure that the supplied pipeline
     meets the nf-core guidelines. Documentation of all lint tests can be found
-    on the nf-core website: https://nf-co.re/errors
+    on the nf-core website: https://nf-co.re/tools-docs/
+
+    You can ignore tests using a file called .nf-core-lint.yaml (if you have a good reason!).
+    See the documentation for details.
     """
 
     # Run the lint tests!

nf_core/pipeline-template/lib/NfcoreSchema.groovy

@@ -191,11 +191,11 @@ class NfcoreSchema {
 
     // Remove an element from a JSONArray
     private static JSONArray removeElement(jsonArray, element){
-        def list = []  
+        def list = []
         int len = jsonArray.length()
-        for (int i=0;i<len;i++){ 
+        for (int i=0;i<len;i++){
             list.add(jsonArray.get(i).toString())
-        } 
+        }
         list.remove(element)
         JSONArray jsArray = new JSONArray(list)
         return jsArray
@@ -213,7 +213,7 @@ class NfcoreSchema {
                             // If the param was required, change this
                             if (definition[key].has("required")) {
                                 def cleaned_required = removeElement(definition[key].required, ignore_param)
-                                definition[key].put("required", cleaned_required) 
+                                definition[key].put("required", cleaned_required)
                             }
                         }
                     }
@@ -482,10 +482,10 @@ class NfcoreSchema {
         }
         workflow_summary['runName']      = workflow.runName
         if (workflow.containerEngine) {
-            workflow_summary['containerEngine'] = "$workflow.containerEngine"
+            workflow_summary['containerEngine'] = workflow.containerEngine
         }
         if (workflow.container) {
-            workflow_summary['container']       = "$workflow.container"
+            workflow_summary['container'] = workflow.container
         }
         workflow_summary['launchDir']    = workflow.launchDir
         workflow_summary['workDir']      = workflow.workDir
@@ -506,17 +506,7 @@ class NfcoreSchema {
                     def params_value = params.get(param)
                     def schema_value = group_params.get(param).default
                     def param_type   = group_params.get(param).type
-                    if (schema_value == null) {
-                        if (param_type == 'boolean') {
-                            schema_value = false
-                        }
-                        if (param_type == 'string') {
-                            schema_value = ''
-                        }
-                        if (param_type == 'integer') {
-                            schema_value = 0
-                        }
-                    } else {
+                    if (schema_value != null) {
                         if (param_type == 'string') {
                             if (schema_value.contains('$projectDir') || schema_value.contains('${projectDir}')) {
                                 def sub_string = schema_value.replace('\$projectDir', '')
@@ -535,8 +525,13 @@ class NfcoreSchema {
                         }
                     }
 
-                    if (params_value != schema_value) {
-                        sub_params.put("$param", params_value)
+                    // We have a default in the schema, and this isn't it
+                    if (schema_value != null && params_value != schema_value) {
+                        sub_params.put(param, params_value)
+                    }
+                    // No default in the schema, and this isn't empty
+                    else if (schema_value == null && params_value != "" && params_value != null && params_value != false) {
+                        sub_params.put(param, params_value)
                     }
                 }
             }
@@ -549,22 +544,23 @@ class NfcoreSchema {
      * Beautify parameters for summary and return as string
      */
     private static String params_summary_log(workflow, params, json_schema) {
+        Map colors = log_colours(params.monochrome_logs)
         String output  = ''
         def params_map = params_summary_map(workflow, params, json_schema)
         def max_chars  = params_max_chars(params_map)
         for (group in params_map.keySet()) {
             def group_params = params_map.get(group)  // This gets the parameters of that particular group
             if (group_params) {
-                output += group + '\n'
+                output += colors.bold + group + colors.reset + '\n'
                 for (param in group_params.keySet()) {
-                    output += "    \u001B[1m" +  param.padRight(max_chars) + ": \u001B[1m" + group_params.get(param) + '\n'
+                    output += "  " + colors.blue + param.padRight(max_chars) + ": " + colors.green +  group_params.get(param) + colors.reset + '\n'
                 }
                 output += '\n'
             }
         }
-        output += "[Only displaying parameters that differ from pipeline default]\n"
         output += dashed_line(params.monochrome_logs)
-        output += '\n\n' + dashed_line(params.monochrome_logs)
+        output += colors.dim + "\n Only displaying parameters that differ from defaults.\n" + colors.reset
+        output += dashed_line(params.monochrome_logs)
         return output
     }
 

nf_core/pipeline-template/nextflow.config

@@ -129,21 +129,22 @@ env {
 // Capture exit codes from upstream processes when piping
 process.shell = ['/bin/bash', '-euo', 'pipefail']
 
+def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
 timeline {
   enabled = true
-  file = "${params.tracedir}/execution_timeline.html"
+  file = "${params.tracedir}/execution_timeline_${trace_timestamp}.html"
 }
 report {
   enabled = true
-  file = "${params.tracedir}/execution_report.html"
+  file = "${params.tracedir}/execution_report_${trace_timestamp}.html"
 }
 trace {
   enabled = true
-  file = "${params.tracedir}/execution_trace.txt"
+  file = "${params.tracedir}/execution_trace_${trace_timestamp}.txt"
 }
 dag {
   enabled = true
-  file = "${params.tracedir}/pipeline_dag.svg"
+  file = "${params.tracedir}/pipeline_dag_${trace_timestamp}.svg"
 }
 
 manifest {