Fix linting (back to tools 2.10 template)

.github/CONTRIBUTING.md

@@ -27,9 +27,6 @@ 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

@@ -19,7 +19,6 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/crea
 - [ ] If necessary, also make a PR on the nf-core/createtaxdb _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/linting.yml

@@ -14,9 +14,9 @@ jobs:
   EditorConfig:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v3
 
-      - uses: actions/setup-node@v4
+      - uses: actions/setup-node@v3
 
       - name: Install editorconfig-checker
         run: npm install -g editorconfig-checker
@@ -27,9 +27,9 @@ jobs:
   Prettier:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v3
 
-      - uses: actions/setup-node@v4
+      - uses: actions/setup-node@v3
 
       - name: Install Prettier
         run: npm install -g prettier
@@ -40,7 +40,7 @@ jobs:
   PythonBlack:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v3
 
       - name: Check code lints with Black
         uses: psf/black@stable
@@ -71,14 +71,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v4
+        uses: actions/checkout@v3
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
 
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.12"
+          python-version: "3.11"
           architecture: "x64"
 
       - name: Install dependencies

lib/NfcoreTemplate.groovy

@@ -4,7 +4,6 @@
 
 import org.yaml.snakeyaml.Yaml
 import groovy.json.JsonOutput
-import nextflow.extension.FilesEx
 
 class NfcoreTemplate {
 
@@ -142,14 +141,12 @@ 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 != null && mqc_report.size() <= max_multiqc_email_size.toBytes() ) {
+                if ( mqc_report.size() <= max_multiqc_email_size.toBytes() ) {
                     mail_cmd += [ '-A', mqc_report ]
                 }
                 mail_cmd.execute() << email_html
@@ -158,16 +155,14 @@ class NfcoreTemplate {
         }
 
         // Write summary e-mail HTML to a file
-        def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html")
+        def output_d = new File("${params.outdir}/pipeline_info/")
+        if (!output_d.exists()) {
+            output_d.mkdirs()
+        }
+        def output_hf = new File(output_d, "pipeline_report.html")
         output_hf.withWriter { w -> w << email_html }
-        FilesEx.copyTo(output_hf.toPath(), "${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")
+        def output_tf = new File(output_d, "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()
     }
 
     //
@@ -232,14 +227,15 @@ class NfcoreTemplate {
     // Dump pipeline parameters in a json file
     //
     public static void dump_parameters(workflow, params) {
+        def output_d = new File("${params.outdir}/pipeline_info/")
+        if (!output_d.exists()) {
+            output_d.mkdirs()
+        }
+
         def timestamp  = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
-        def filename   = "params_${timestamp}.json"
-        def temp_pf    = new File(workflow.launchDir.toString(), ".${filename}")
+        def output_pf  = new File(output_d, "params_${timestamp}.json")
         def jsonStr    = JsonOutput.toJson(params)
-        temp_pf.text   = JsonOutput.prettyPrint(jsonStr)
-
-        FilesEx.copyTo(temp_pf.toPath(), "${params.outdir}/pipeline_info/params_${timestamp}.json")
-        temp_pf.delete()
+        output_pf.text = JsonOutput.prettyPrint(jsonStr)
     }
 
     //