Merge pull request #3126 from mirpedrol/template-customisation-email

Template: add option to exclude email from pipeline template

CHANGELOG.md

@@ -18,6 +18,7 @@
 - handle template features with a yaml file ([#3108](https://github.com/nf-core/tools/pull/3108))
 - add templatefeatures.yml to python package ([#3112](https://github.com/nf-core/tools/pull/3112))
 - add option to exclude license from pipeline template ([#3125](https://github.com/nf-core/tools/pull/3125))
+- add option to exclude email from pipeline template ([#3126](https://github.com/nf-core/tools/pull/3126))
 
 ### Linting
 

nf_core/pipeline-template/.editorconfig

@@ -25,8 +25,10 @@ insert_final_newline = unset
 trim_trailing_whitespace = unset
 indent_style = unset
 
+{%- if email %}
 [/assets/email*]
 indent_size = unset
+{%- endif %}
 
 # ignore python and markdown
 [*.{py,md}]

nf_core/pipeline-template/.prettierignore

@@ -1,4 +1,6 @@
+{%- if email %}
 email_template.html
+{%- endif %}
 adaptivecard.json
 slackreport.json
 .nextflow*

nf_core/pipeline-template/docs/output.md

@@ -55,7 +55,7 @@ Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQ
 
 - `pipeline_info/`
   - Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`.
-  - Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline.
+    {% if email %}- Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline. {% endif %}
   - Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`.
   - Parameters used by the pipeline run: `params.json`.
 

nf_core/pipeline-template/main.nf

@@ -20,7 +20,7 @@
 include { {{ short_name|upper }}  } from './workflows/{{ short_name }}'
 include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'
 include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'
-{% if igenomes %}
+{%- if igenomes %}
 include { getGenomeAttribute      } from './subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'
 
 /*
@@ -95,9 +95,11 @@ workflow {
     // SUBWORKFLOW: Run completion tasks
     //
     PIPELINE_COMPLETION (
+        {%- if email %}
         params.email,
         params.email_on_fail,
         params.plaintext_email,
+        {%- endif %}
         params.outdir,
         params.monochrome_logs,
         params.hook_url,

nf_core/pipeline-template/nextflow.config

@@ -32,9 +32,11 @@ params {
     // Boilerplate options
     outdir                       = null
     publish_dir_mode             = 'copy'
+    {%- if email %}
     email                        = null
     email_on_fail                = null
     plaintext_email              = false
+    {%- endif %}
     monochrome_logs              = false
     hook_url                     = null
     help                         = false

nf_core/pipeline-template/nextflow_schema.json

@@ -28,14 +28,14 @@
                     "format": "directory-path",
                     "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
                     "fa_icon": "fas fa-folder-open"
-                },
+                }{% if email %},
                 "email": {
                     "type": "string",
                     "description": "Email address for completion summary.",
                     "fa_icon": "fas fa-envelope",
                     "help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
                     "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
-                }{% if multiqc %},
+                }{% endif %}{% if multiqc %},
                 "multiqc_title": {
                     "type": "string",
                     "description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.",
@@ -189,7 +189,7 @@
                     "fa_icon": "fas fa-copy",
                     "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
                     "hidden": true
-                },
+                },{% if email %}
                 "email_on_fail": {
                     "type": "string",
                     "description": "Email address for completion summary, only when pipeline fails.",
@@ -203,7 +203,7 @@
                     "description": "Send plain-text email instead of HTML.",
                     "fa_icon": "fas fa-remove-format",
                     "hidden": true
-                },
+                },{% endif %}
                 {%- if multiqc %}
                 "max_multiqc_email_size": {
                     "type": "string",

nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf

@@ -12,7 +12,9 @@ include { UTILS_NFVALIDATION_PLUGIN } from '../../nf-core/utils_nfvalidation_plu
 include { paramsSummaryMap          } from 'plugin/nf-validation'
 include { fromSamplesheet           } from 'plugin/nf-validation'
 include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
+{%- if email %}
 include { completionEmail           } from '../../nf-core/utils_nfcore_pipeline'
+{%- endif %}
 include { completionSummary         } from '../../nf-core/utils_nfcore_pipeline'
 include { dashedLine                } from '../../nf-core/utils_nfcore_pipeline'
 include { nfCoreLogo                } from '../../nf-core/utils_nfcore_pipeline'
@@ -117,9 +119,11 @@ workflow PIPELINE_INITIALISATION {
 workflow PIPELINE_COMPLETION {
 
     take:
+    {%- if email %}
     email           //  string: email address
     email_on_fail   //  string: email address sent on pipeline failure
     plaintext_email // boolean: Send plain-text email instead of HTML
+    {% endif %}
     outdir          //    path: Path to output directory where results will be published
     monochrome_logs // boolean: Disable ANSI colour codes in log output
     hook_url        //  string: hook URL for notifications
@@ -133,13 +137,15 @@ workflow PIPELINE_COMPLETION {
     // Completion email and summary
     //
     workflow.onComplete {
+        {%- if email %}
         if (email || email_on_fail) {
             {%- if multiqc %}
             completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs, multiqc_report.toList())
             {%- else %}
             completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs, [])
             {%- endif %}
         }
+        {%- endif %}
 
         completionSummary(monochrome_logs)
 

nf_core/pipelines/create/templatefeatures.yml

@@ -257,3 +257,21 @@ license:
       - "LICENSE"
   nfcore_pipelines: False
   custom_pipelines: True
+email:
+  skippable_paths:
+    - "assets/email_template.html"
+    - "assets/sendmail_template.txt"
+    - "assets/email_template.txt"
+  short_description: "Enable email updates"
+  description: "Enable sending emails on pipeline completion."
+  help_text: |
+    Enable the option of sending an email which will include pipeline execution reports on pipeline completion.
+  linting:
+    files_exist:
+      - "assets/email_template.html"
+      - "assets/sendmail_template.txt"
+      - "assets/email_template.txt"
+    files_unchanged:
+      - ".prettierignore"
+  nfcore_pipelines: False
+  custom_pipelines: True