Merge branch 'TEMPLATE' into dev_template

.github/CONTRIBUTING.md

@@ -27,6 +27,9 @@ If you're not used to this workflow with git, you can start with some [docs from
 
 ## Tests
 
+You can optionally test your changes by running the pipeline locally. Then it is recommended to use the `debug` profile to
+receive warnings about process selectors and other debug info. Example: `nextflow run . -profile debug,test,docker --outdir <OUTDIR>`.
+
 When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests.
 Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then.
 

.github/PULL_REQUEST_TEMPLATE.md

@@ -19,6 +19,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/vira
 - [ ] If necessary, also make a PR on the nf-core/viralrecon _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
+- [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
 - [ ] Output Documentation in `docs/output.md` is updated.
 - [ ] `CHANGELOG.md` is updated.

.github/workflows/ci.yml

@@ -28,7 +28,7 @@ jobs:
           - "latest-everything"
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1

.github/workflows/fix-linting.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -24,7 +24,7 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
 
       - name: Install Prettier
         run: npm install -g prettier @prettier/plugin-php

.github/workflows/linting.yml

@@ -14,9 +14,9 @@ jobs:
   EditorConfig:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
 
       - name: Install editorconfig-checker
         run: npm install -g editorconfig-checker
@@ -27,9 +27,9 @@ jobs:
   Prettier:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
 
       - name: Install Prettier
         run: npm install -g prettier
@@ -40,7 +40,7 @@ jobs:
   PythonBlack:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Check code lints with Black
         uses: psf/black@stable
@@ -71,7 +71,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1

.gitpod.yml

@@ -4,7 +4,9 @@ tasks:
     command: |
       pre-commit install --install-hooks
       nextflow self-update
-
+  - name: unset JAVA_TOOL_OPTIONS
+    command: |
+      unset JAVA_TOOL_OPTIONS
 vscode:
   extensions: # based on nf-core.nf-core-extensionpack
     - codezombiech.gitignore # Language support for .gitignore files

README.md

@@ -146,11 +146,9 @@ nextflow run nf-core/viralrecon \
    -profile -profile <docker/singularity/.../institute>
 ```
 
-:::warning
-Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those
-provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;
-see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
-:::
+> [!WARNING]
+> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;
+> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
 
 For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/viralrecon/usage) and the [parameter documentation](https://nf-co.re/viralrecon/parameters).
 

assets/slackreport.json

@@ -3,7 +3,7 @@
         {
             "fallback": "Plain-text summary of the attachment.",
             "color": "<% if (success) { %>good<% } else { %>danger<%} %>",
-            "author_name": "nf-core/viralrecon v${version} - ${runName}",
+            "author_name": "nf-core/viralrecon ${version} - ${runName}",
             "author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico",
             "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>",
             "fields": [

conf/modules.config

@@ -39,7 +39,7 @@ process {
 }
 
     withName: 'MULTIQC' {
-        ext.args   = params.multiqc_title ? "--title \"$params.multiqc_title\"" : ''
+        ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
         publishDir = [
             path: { "${params.outdir}/multiqc" },
             mode: params.publish_dir_mode,

docs/usage.md

@@ -18,9 +18,9 @@ You will need to create a samplesheet with information about the samples you wou
 --input '[path to samplesheet file]'
 ```
 
-The `sample` identifiers have to be the same when you have re-sequenced the same sample more than once (e.g. to increase sequencing depth). The pipeline will concatenate the raw reads before performing any downstream analysis.
+### Multiple runs of the same sample
 
-A final samplesheet file may look something like the one below. `SAMPLE_1` was sequenced twice in Illumina PE format, `SAMPLE_2` was sequenced once in Illumina SE format.
+The `sample` identifiers have to be the same when you have re-sequenced the same sample more than once e.g. to increase sequencing depth. The pipeline will concatenate the raw reads before performing any downstream analysis. Below is an example for the same sample sequenced across 3 lanes:
 
 ```console
 sample,fastq_1,fastq_2

lib/NfcoreTemplate.groovy

@@ -4,6 +4,7 @@
 
 import org.yaml.snakeyaml.Yaml
 import groovy.json.JsonOutput
+import nextflow.extension.FilesEx
 
 class NfcoreTemplate {
 
@@ -159,12 +160,14 @@ class NfcoreTemplate {
             try {
                 if (params.plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') }
                 // Try to send HTML e-mail using sendmail
+                def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html")
+                sendmail_tf.withWriter { w -> w << sendmail_html }
                 [ 'sendmail', '-t' ].execute() << sendmail_html
                 log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-"
             } catch (all) {
                 // Catch failures and try with plaintext
                 def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ]
-                if ( mqc_report.size() <= max_multiqc_email_size.toBytes() ) {
+                if ( mqc_report != null && mqc_report.size() <= max_multiqc_email_size.toBytes() ) {
                     mail_cmd += [ '-A', mqc_report ]
                 }
                 mail_cmd.execute() << email_html
@@ -173,14 +176,16 @@ class NfcoreTemplate {
         }
 
         // Write summary e-mail HTML to a file
-        def output_d = new File("${params.outdir}/pipeline_info/")
-        if (!output_d.exists()) {
-            output_d.mkdirs()
-        }
-        def output_hf = new File(output_d, "pipeline_report.html")
+        def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html")
         output_hf.withWriter { w -> w << email_html }
-        def output_tf = new File(output_d, "pipeline_report.txt")
+        FilesEx.copyTo(output_hf.toPath(), "${params.outdir}/pipeline_info/pipeline_report.html");
+        output_hf.delete()
+
+        // Write summary e-mail TXT to a file
+        def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt")
         output_tf.withWriter { w -> w << email_txt }
+        FilesEx.copyTo(output_tf.toPath(), "${params.outdir}/pipeline_info/pipeline_report.txt");
+        output_tf.delete()
     }
 
     //
@@ -245,15 +250,14 @@ class NfcoreTemplate {
     // Dump pipeline parameters in a json file
     //
     public static void dump_parameters(workflow, params) {
-        def output_d = new File("${params.outdir}/pipeline_info/")
-        if (!output_d.exists()) {
-            output_d.mkdirs()
-        }
-
         def timestamp  = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
-        def output_pf  = new File(output_d, "params_${timestamp}.json")
+        def filename   = "params_${timestamp}.json"
+        def temp_pf    = new File(workflow.launchDir.toString(), ".${filename}")
         def jsonStr    = JsonOutput.toJson(params)
-        output_pf.text = JsonOutput.prettyPrint(jsonStr)
+        temp_pf.text   = JsonOutput.prettyPrint(jsonStr)
+
+        FilesEx.copyTo(temp_pf.toPath(), "${params.outdir}/pipeline_info/params_${timestamp}.json")
+        temp_pf.delete()
     }
 
     //