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New course: Nextflow Triathlon: plain Nextflow + nf-core + Seqera platform#951

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New course: Nextflow Triathlon: plain Nextflow + nf-core + Seqera platform#951
vdauwera wants to merge 20 commits into
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@vdauwera

@vdauwera vdauwera commented May 8, 2026

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Creates a new training course (docs/en/docs/nextflow_triathlon/) designed as a fast-track introduction to the Nextflow ecosystem. The course covers three topics in sequence:

  • Part 1 (~45 min): Condensed version of Nextflow Run parts 1 & 2 — running pipelines, the work/ directory, -resume, channels, multi-step workflows, and containers.
  • Part 2 (~45 min): Adapted from Hello nf-core part 1 — finding and running nf-core pipelines, parameter and input validation, custom configuration, plus a new section running nf-core/rnaseq with the test profile as a bridge to Part 3.
  • Part 3 (~45 min): New content for Seqera Platform — launching nf-core/rnaseq from the Seqera Pipelines catalog at production scale (based on the Seqera Platform getting-started tutorial), then adding nf-core/demo from GitHub to demonstrate the bring-your-own-pipeline workflow.

Also includes orientation, next steps, and survey pages, mkdocs.yml nav and plugin config updates, and a note in the orientation to upgrade the Codespaces machine to 8 cores for parallel execution demos.

@vdauwera vdauwera self-assigned this May 8, 2026
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@vdauwera vdauwera changed the title First pass of the triathlon course New course: Nextflow Triathlon: plain Nextflow + nf-core + Seqera platform May 8, 2026
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Nextflow linting complete!

⚠️ 24 files had 53 warnings
✅ 189 files had no errors
🔧 136 files would be changed by auto-formatting

💡 Tip: Click filename locations to go directly to that code.

View all 53 issues
Type Location Message
Warning hello-nf-core/solutions/core-hello-part2/subworkflows/local/utils_nfcore_hello_pipeline/main.nf:30:5 Parameter was not used -- prefix with _ to suppress warning
Warning hello-nf-core/solutions/core-hello-part2/subworkflows/local/utils_nfcore_hello_pipeline/main.nf:33:5 Parameter was not used -- prefix with _ to suppress warning
Warning hello-nf-core/solutions/core-hello-part2/subworkflows/local/utils_nfcore_hello_pipeline/main.nf:98:5 Parameter was not used -- prefix with _ to suppress warning
Warning hello-nf-core/solutions/core-hello-part2/subworkflows/local/utils_nfcore_hello_pipeline/main.nf:102:5 Variable was declared but not used
Warning hello-nf-core/solutions/core-hello-part2/subworkflows/nf-core/utils_nfcore_pipeline/main.nf:16:5 Variable was declared but not used
Warning hello-nf-core/solutions/core-hello-part2/workflows/hello.nf:43:26 The use of Channel to access channel factories is deprecated -- use channel instead
Warning hello-nf-core/solutions/core-hello-part2/workflows/hello.nf:67:17 Variable was declared but not used
Warning hello-nf-core/solutions/core-hello-part3/subworkflows/local/utils_nfcore_hello_pipeline/main.nf:30:5 Parameter was not used -- prefix with _ to suppress warning
Warning hello-nf-core/solutions/core-hello-part3/subworkflows/local/utils_nfcore_hello_pipeline/main.nf:33:5 Parameter was not used -- prefix with _ to suppress warning
Warning hello-nf-core/solutions/core-hello-part3/subworkflows/local/utils_nfcore_hello_pipeline/main.nf:98:5 Parameter was not used -- prefix with _ to suppress warning
Warning hello-nf-core/solutions/core-hello-part3/subworkflows/local/utils_nfcore_hello_pipeline/main.nf:102:5 Variable was declared but not used
Warning hello-nf-core/solutions/core-hello-part3/subworkflows/nf-core/utils_nfcore_pipeline/main.nf:16:5 Variable was declared but not used
Warning hello-nf-core/solutions/core-hello-part3/workflows/hello.nf:44:55 Parameter was not used -- prefix with _ to suppress warning
Warning hello-nf-core/solutions/core-hello-part3/workflows/hello.nf:52:26 The use of Channel to access channel factories is deprecated -- use channel instead
Warning hello-nf-core/solutions/core-hello-part3/workflows/hello.nf:76:17 Variable was declared but not used
Warning hello-nf-core/solutions/core-hello-part4/modules/local/cowpy/main.nf:30:9 Variable was declared but not used
Warning hello-nf-core/solutions/core-hello-part4/subworkflows/local/utils_nfcore_hello_pipeline/main.nf:30:5 Parameter was not used -- prefix with _ to suppress warning
Warning hello-nf-core/solutions/core-hello-part4/subworkflows/local/utils_nfcore_hello_pipeline/main.nf:33:5 Parameter was not used -- prefix with _ to suppress warning
Warning hello-nf-core/solutions/core-hello-part4/subworkflows/local/utils_nfcore_hello_pipeline/main.nf:98:5 Parameter was not used -- prefix with _ to suppress warning
Warning hello-nf-core/solutions/core-hello-part4/subworkflows/local/utils_nfcore_hello_pipeline/main.nf:102:5 Variable was declared but not used
Warning hello-nf-core/solutions/core-hello-part4/subworkflows/nf-core/utils_nfcore_pipeline/main.nf:16:5 Variable was declared but not used
Warning hello-nf-core/solutions/core-hello-part4/workflows/hello.nf:49:26 The use of Channel to access channel factories is deprecated -- use channel instead
Warning hello-nf-core/solutions/core-hello-part4/workflows/hello.nf:73:17 Variable was declared but not used
Warning hello-nf-core/solutions/core-hello-part5/modules/local/cowpy/main.nf:30:9 Variable was declared but not used
Warning hello-nf-core/solutions/core-hello-part5/subworkflows/local/utils_nfcore_hello_pipeline/main.nf:30:5 Parameter was not used -- prefix with _ to suppress warning
Warning hello-nf-core/solutions/core-hello-part5/subworkflows/local/utils_nfcore_hello_pipeline/main.nf:33:5 Parameter was not used -- prefix with _ to suppress warning
Warning hello-nf-core/solutions/core-hello-part5/subworkflows/local/utils_nfcore_hello_pipeline/main.nf:97:5 Parameter was not used -- prefix with _ to suppress warning
Warning hello-nf-core/solutions/core-hello-part5/subworkflows/local/utils_nfcore_hello_pipeline/main.nf:101:5 Variable was declared but not used
Warning hello-nf-core/solutions/core-hello-part5/subworkflows/nf-core/utils_nfcore_pipeline/main.nf:16:5 Variable was declared but not used
Warning hello-nf-core/solutions/core-hello-part5/workflows/hello.nf:49:26 The use of Channel to access channel factories is deprecated -- use channel instead
Warning hello-nf-core/solutions/core-hello-part5/workflows/hello.nf:73:17 Variable was declared but not used
Warning hello-nf-core/solutions/core-hello-start/subworkflows/local/utils_nfcore_hello_pipeline/main.nf:29:5 Parameter was not used -- prefix with _ to suppress warning
Warning hello-nf-core/solutions/core-hello-start/subworkflows/local/utils_nfcore_hello_pipeline/main.nf:32:5 Parameter was not used -- prefix with _ to suppress warning
Warning hello-nf-core/solutions/core-hello-start/subworkflows/local/utils_nfcore_hello_pipeline/main.nf:68:5 The use of Channel to access channel factories is deprecated -- use channel instead
Warning hello-nf-core/solutions/core-hello-start/subworkflows/local/utils_nfcore_hello_pipeline/main.nf:102:5 Parameter was not used -- prefix with _ to suppress warning
Warning hello-nf-core/solutions/core-hello-start/subworkflows/local/utils_nfcore_hello_pipeline/main.nf:106:5 Variable was declared but not used
Warning hello-nf-core/solutions/core-hello-start/subworkflows/nf-core/utils_nfcore_pipeline/main.nf:16:5 Variable was declared but not used
Warning hello-nf-core/solutions/core-hello-start/workflows/hello.nf:18:5 Parameter was not used -- prefix with _ to suppress warning
Warning hello-nf-core/solutions/core-hello-start/workflows/hello.nf:26:26 The use of Channel to access channel factories is deprecated -- use channel instead
Warning hello-nf-core/solutions/core-hello-start/workflows/hello.nf:50:17 Variable was declared but not used
Warning side-quests/solutions/debugging/buggy_workflow.nf:91:44 Implicit closure parameter is deprecated, declare an explicit parameter instead
Warning side-quests/solutions/essential_scripting_patterns/main.nf:59:25 Parameter was not used -- prefix with _ to suppress warning
Warning side-quests/solutions/essential_scripting_patterns/main.nf:63:53 Parameter was not used -- prefix with _ to suppress warning
Warning side-quests/solutions/essential_scripting_patterns/main.nf:68:5 Variable was declared but not used
Warning side-quests/solutions/essential_scripting_patterns/main.nf:69:5 Variable was declared but not used
Warning side-quests/solutions/metadata/1.2/main.nf:5:5 Variable was declared but not used
Warning side-quests/solutions/metadata/2.4/main.nf:42:22 Parameter was not used -- prefix with _ to suppress warning
Warning side-quests/solutions/metadata/3.2/main.nf:42:22 Parameter was not used -- prefix with _ to suppress warning
Warning side-quests/solutions/splitting_and_grouping/main.nf:11:25 Parameter was not used -- prefix with _ to suppress warning
Warning side-quests/solutions/splitting_and_grouping/main.nf:14:25 Parameter was not used -- prefix with _ to suppress warning
Warning side-quests/solutions/splitting_and_grouping/main.nf:29:5 Variable was declared but not used
Warning side-quests/solutions/working_with_files/6/main.nf:10:43 Variable was declared but not used
Warning side-quests/solutions/working_with_files/6/main.nf:30:22 Parameter was not used -- prefix with _ to suppress warning
View formatting changes <...*[Comment body truncated]*
FileDiff
hello-nextflow/solutions/1-hello-world/hello-world-2.nf
View 
@@ -4,7 +4,6 @@
  * Use echo to print 'Hello World!' to a file
  */
 process sayHello {
-
     output:
     path 'output.txt'
hello-nextflow/solutions/1-hello-world/hello-world-3.nf
View 
@@ -4,7 +4,6 @@
  * Use echo to print 'Hello World!' to a file
  */
 process sayHello {
-
     input:
     val greeting
hello-nextflow/solutions/2-hello-channels/hello-channels-1.nf
View 
@@ -4,7 +4,6 @@
  * Use echo to print 'Hello World!' to a file
  */
 process sayHello {
-
     input:
     val greeting
 
@@ -29,7 +28,7 @@ workflow {
     main:
     // create a channel for inputs
     greeting_ch = channel.of('Hello Channels!')
-                        .view()
+        .view()
     // emit a greeting
... (truncated)
hello-nextflow/solutions/2-hello-channels/hello-channels-2.nf
View 
@@ -4,7 +4,6 @@
  * Use echo to print 'Hello World!' to a file
  */
 process sayHello {
-
     input:
     val greeting
 
@@ -29,7 +28,7 @@ workflow {
     main:
     // create a channel for inputs
     greeting_ch = channel.of('Hello', 'Bonjour', 'Hola')
-                        .view()
+        .view()
     // emit a greeting
... (truncated)
hello-nextflow/solutions/2-hello-channels/hello-channels-3.nf
View 
@@ -4,7 +4,6 @@
  * Use echo to print 'Hello World!' to a file
  */
 process sayHello {
-
     input:
     val greeting
 
@@ -28,12 +27,12 @@ workflow {
 
     main:
     // declare an array of input greetings
-    greetings_array = ['Hello','Bonjour','Hola']
+    greetings_array = ['Hello', 'Bonjour', 'Hola']
     // create a channel for inputs
... (truncated)
hello-nextflow/solutions/2-hello-channels/hello-channels-4.nf
View 
@@ -4,7 +4,6 @@
  * Use echo to print 'Hello World!' to a file
  */
 process sayHello {
-
     input:
     val greeting
 
@@ -29,11 +28,11 @@ workflow {
     main:
     // create a channel for inputs from a CSV file
     greeting_ch = channel.fromPath(params.input)
-                        .view { csv -> "Before splitCsv: $csv" }
-                        .splitCsv()
-                        .view { csv -> "After splitCsv: $csv" }
... (truncated)
hello-nextflow/solutions/3-hello-workflow/hello-workflow-1.nf
View 
@@ -4,7 +4,6 @@
  * Use echo to print 'Hello World!' to a file
  */
 process sayHello {
-
     input:
     val greeting
 
@@ -21,7 +20,6 @@ process sayHello {
  * Use a text replacement tool to convert the greeting to uppercase
  */
 process convertToUpper {
-
     input:
     path input_file
... (truncated)
hello-nextflow/solutions/3-hello-workflow/hello-workflow-2.nf
View 
@@ -4,7 +4,6 @@
  * Use echo to print 'Hello World!' to a file
  */
 process sayHello {
-
     input:
     val greeting
 
@@ -21,7 +20,6 @@ process sayHello {
  * Use a text replacement tool to convert the greeting to uppercase
  */
 process convertToUpper {
-
     input:
     path input_file
... (truncated)
hello-nextflow/solutions/3-hello-workflow/hello-workflow-3.nf
View 
@@ -4,7 +4,6 @@
  * Use echo to print 'Hello World!' to a file
  */
 process sayHello {
-
     input:
     val greeting
 
@@ -21,7 +20,6 @@ process sayHello {
  * Use a text replacement tool to convert the greeting to uppercase
  */
 process convertToUpper {
-
     input:
     path input_file
... (truncated)
hello-nextflow/solutions/3-hello-workflow/hello-workflow-4.nf
View 
@@ -4,7 +4,6 @@
  * Use echo to print 'Hello World!' to a file
  */
 process sayHello {
-
     input:
     val greeting
 
@@ -21,7 +20,6 @@ process sayHello {
  * Use a text replacement tool to convert the greeting to uppercase
  */
 process convertToUpper {
-
     input:
     path input_file
... (truncated)
hello-nextflow/solutions/4-hello-modules/hello-modules-2.nf
View 
@@ -7,7 +7,6 @@ include { sayHello } from './modules/sayHello.nf'
  * Use a text replacement tool to convert the greeting to uppercase
  */
 process convertToUpper {
-
     input:
     path input_file
 
@@ -24,7 +23,6 @@ process convertToUpper {
  * Collect uppercase greetings into a single output file
  */
 process collectGreetings {
-
     input:
     path input_files
... (truncated)
hello-nextflow/solutions/4-hello-modules/hello-modules-3.nf
View 
@@ -8,7 +8,6 @@ include { convertToUpper } from './modules/convertToUpper.nf'
  * Collect uppercase greetings into a single output file
  */
 process collectGreetings {
-
     input:
     path input_files
     val batch_name
@@ -38,8 +37,8 @@ workflow {
     main:
     // create a channel for inputs from a CSV file
     greeting_ch = channel.fromPath(params.input)
-                        .splitCsv()
-                        .map { line -> line[0] }
+        .splitCsv()
... (truncated)
hello-nextflow/solutions/4-hello-modules/hello-modules-4.nf
View 
@@ -18,8 +18,8 @@ workflow {
     main:
     // create a channel for inputs from a CSV file
     greeting_ch = channel.fromPath(params.input)
-                        .splitCsv()
-                        .map { line -> line[0] }
+        .splitCsv()
+        .map { line -> line[0] }
     // emit a greeting
     sayHello(greeting_ch)
     // convert the greeting to uppercase
hello-nextflow/solutions/4-hello-modules/modules/collectGreetings.nf
View 
@@ -2,7 +2,6 @@
  * Collect uppercase greetings into a single output file
  */
 process collectGreetings {
-
     input:
     path input_files
     val batch_name
hello-nextflow/solutions/4-hello-modules/modules/convertToUpper.nf
View 
@@ -2,7 +2,6 @@
  * Use a text replacement tool to convert the greeting to uppercase
  */
 process convertToUpper {
-
     input:
     path input_file
hello-nextflow/solutions/4-hello-modules/modules/sayHello.nf
View 
@@ -2,7 +2,6 @@
  * Use echo to print 'Hello World!' to a file
  */
 process sayHello {
-
     input:
     val greeting
hello-nextflow/solutions/5-hello-containers/hello-containers-2.nf
View 
@@ -20,8 +20,8 @@ workflow {
     main:
     // create a channel for inputs from a CSV file
     greeting_ch = channel.fromPath(params.input)
-                        .splitCsv()
-                        .map { line -> line[0] }
+        .splitCsv()
+        .map { line -> line[0] }
     // emit a greeting
     sayHello(greeting_ch)
     // convert the greeting to uppercase
hello-nextflow/solutions/5-hello-containers/modules/collectGreetings.nf
View 
@@ -2,7 +2,6 @@
  * Collect uppercase greetings into a single output file
  */
 process collectGreetings {
-
     input:
     path input_files
     val batch_name
hello-nextflow/solutions/5-hello-containers/modules/convertToUpper.nf
View 
@@ -2,7 +2,6 @@
  * Use a text replacement tool to convert the greeting to uppercase
  */
 process convertToUpper {
-
     input:
     path input_file
hello-nextflow/solutions/5-hello-containers/modules/sayHello.nf
View 
@@ -2,7 +2,6 @@
  * Use echo to print 'Hello World!' to a file
  */
 process sayHello {
-
     input:
     val greeting
hello-nextflow/solutions/6-hello-config/hello-config.nf
View 
@@ -20,8 +20,8 @@ workflow {
     main:
     // create a channel for inputs from a CSV file
     greeting_ch = channel.fromPath(params.input)
-                        .splitCsv()
-                        .map { line -> line[0] }
+        .splitCsv()
+        .map { line -> line[0] }
     // emit a greeting
     sayHello(greeting_ch)
     // convert the greeting to uppercase
hello-nextflow/solutions/6-hello-config/modules/collectGreetings.nf
View 
@@ -2,7 +2,6 @@
  * Collect uppercase greetings into a single output file
  */
 process collectGreetings {
-
     input:
     path input_files
     val batch_name
hello-nextflow/solutions/6-hello-config/modules/convertToUpper.nf
View 
@@ -2,7 +2,6 @@
  * Use a text replacement tool to convert the greeting to uppercase
  */
 process convertToUpper {
-
     input:
     path input_file
hello-nextflow/solutions/6-hello-config/modules/sayHello.nf
View 
@@ -2,7 +2,6 @@
  * Use echo to print 'Hello World!' to a file
  */
 process sayHello {
-
     input:
     val greeting
hello-nextflow/solutions/6-hello-config/nextflow.config
View 
@@ -6,7 +6,7 @@ conda.enabled = true
 */
 process {
     memory = 1.GB
-    withName: 'cowpy' {
+    withName: cowpy {
         memory = 2.GB
         cpus = 2
     }
@@ -32,11 +32,7 @@ profiles {
     univ_hpc {
         process.executor = 'slurm'
         conda.enabled = true
-        process.resourceLimits = [
-            memory: 750.GB,
... (truncated)
hello-nf-core/solutions/composable-hello/hello.nf
View 
@@ -14,9 +14,7 @@ include { collectGreetings } from './modules/collectGreetings.nf'
 include { cowpy } from './modules/cowpy.nf'
 
 workflow HELLO {
-
     take:
-    // channel of greetings
     greeting_ch
 
     main:
hello-nf-core/solutions/composable-hello/main.nf
View 
@@ -9,12 +9,12 @@ params.greeting = 'greetings.csv'
 workflow {
     // create a channel for inputs from a CSV file
     greeting_ch = channel.fromPath(params.greeting)
-                        .splitCsv()
-                        .map { line -> line[0] }
+        .splitCsv()
+        .map { line -> line[0] }
 
     // call the imported workflow on the channel of greetings
     HELLO(greeting_ch)
 
     // view the outputs emitted by the workflow
-    HELLO.out.view { output -> "Output: $output" }
+    HELLO.out.view { output -> "Output: ${output}" }
... (truncated)
hello-nf-core/solutions/composable-hello/modules/collectGreetings.nf
View 
@@ -10,8 +10,8 @@ process collectGreetings {
     val batch_name
 
     output:
-    path "COLLECTED-${batch_name}-output.txt" , emit: outfile
-    val count_greetings , emit: count
+    path "COLLECTED-${batch_name}-output.txt", emit: outfile
+    val count_greetings, emit: count
 
     script:
     count_greetings = input_files.size()
hello-nf-core/solutions/composable-hello/modules/convertToUpper.nf
View 
@@ -13,6 +13,6 @@ process convertToUpper {
 
     script:
     """
-    cat '$input_file' | tr '[a-z]' '[A-Z]' > 'UPPER-${input_file}'
+    cat '${input_file}' | tr '[a-z]' '[A-Z]' > 'UPPER-${input_file}'
     """
 }
hello-nf-core/solutions/composable-hello/modules/cowpy.nf
View 
@@ -15,6 +15,6 @@ process cowpy {
 
     script:
     """
-    cat $input_file | cowpy -c "$character" > cowpy-${input_file}
+    cat ${input_file} | cowpy -c "${character}" > cowpy-${input_file}
     """
 }
hello-nf-core/solutions/composable-hello/modules/sayHello.nf
View 
@@ -13,6 +13,6 @@ process sayHello {
 
     script:
     """
-    echo '$greeting' > '$greeting-output.txt'
+    echo '${greeting}' > '${greeting}-output.txt'
     """
 }
hello-nf-core/solutions/core-hello-part2/conf/base.config
View 
@@ -11,13 +11,13 @@
 process {
 
     // TODO nf-core: Check the defaults for all processes
-    cpus   = { 1      * task.attempt }
-    memory = { 6.GB   * task.attempt }
-    time   = { 4.h    * task.attempt }
+    cpus = { 1 * task.attempt }
+    memory = { 6.GB * task.attempt }
+    time = { 4.h * task.attempt }
 
     errorStrategy = { task.exitStatus in ((130..145) + 104 + 175) ? 'retry' : 'finish' }
-    maxRetries    = 1
-    maxErrors     = '-1'
+    maxRetries = 1
... (truncated)
hello-nf-core/solutions/core-hello-part2/conf/modules.config
View 
@@ -12,10 +12,5 @@
 
 process {
 
-    publishDir = [
-        path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-    ]
-
+    publishDir = [path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }]
 }
hello-nf-core/solutions/core-hello-part2/conf/test.config
View 
@@ -11,21 +11,17 @@
 */
 
 process {
-    resourceLimits = [
-        cpus: 2,
-        memory: '4.GB',
-        time: '1.h'
-    ]
+    resourceLimits = [cpus: 2, memory: '4.GB', time: '1.h']
 }
 
 params {
-    config_profile_name        = 'Test profile'
+    config_profile_name = 'Test profile'
... (truncated)
hello-nf-core/solutions/core-hello-part2/conf/test_full.config
View 
@@ -11,7 +11,7 @@
 */
 
 params {
-    config_profile_name        = 'Full test profile'
+    config_profile_name = 'Full test profile'
     config_profile_description = 'Full test dataset to check pipeline function'
 
     // Input data for full size test
hello-nf-core/solutions/core-hello-part2/main.nf
View 
@@ -13,9 +13,9 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { HELLO  } from './workflows/hello'
+include { HELLO } from './workflows/hello'
 include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_hello_pipeline'
-include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_hello_pipeline'
+include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_hello_pipeline'
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     NAMED WORKFLOWS FOR PIPELINE
@@ -26,7 +26,6 @@ include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_hell
 // WORKFLOW: Run main analysis pipeline depending on type of input
 //
... (truncated)
hello-nf-core/solutions/core-hello-part2/modules/local/collectGreetings.nf
View 
@@ -10,8 +10,8 @@ process collectGreetings {
     val batch_name
 
     output:
-    path "COLLECTED-${batch_name}-output.txt" , emit: outfile
-    val count_greetings , emit: count
+    path "COLLECTED-${batch_name}-output.txt", emit: outfile
+    val count_greetings, emit: count
 
     script:
     count_greetings = input_files.size()
hello-nf-core/solutions/core-hello-part2/modules/local/convertToUpper.nf
View 
@@ -13,6 +13,6 @@ process convertToUpper {
 
     script:
     """
-    cat '$input_file' | tr '[a-z]' '[A-Z]' > 'UPPER-${input_file}'
+    cat '${input_file}' | tr '[a-z]' '[A-Z]' > 'UPPER-${input_file}'
     """
 }
hello-nf-core/solutions/core-hello-part2/modules/local/cowpy.nf
View 
@@ -7,14 +7,14 @@ process cowpy {
     conda 'conda-forge::cowpy==1.1.5'
 
     input:
-        path input_file
-        val character
+    path input_file
+    val character
 
     output:
-        path "cowpy-${input_file}"
+    path "cowpy-${input_file}"
 
     script:
     """
... (truncated)
hello-nf-core/solutions/core-hello-part2/modules/local/sayHello.nf
View 
@@ -13,6 +13,6 @@ process sayHello {
 
     script:
     """
-    echo '$greeting' > '$greeting-output.txt'
+    echo '${greeting}' > '${greeting}-output.txt'
     """
 }
hello-nf-core/solutions/core-hello-part2/nextflow.config
View 
@@ -11,30 +11,30 @@ params {
 
     // TODO nf-core: Specify your pipeline's command line flags
     // Input options
-    input                      = null
+    input = null
 
     // Boilerplate options
-    outdir                       = null
-    publish_dir_mode             = 'copy'
-    monochrome_logs              = false
-    help                         = false
-    help_full                    = false
-    show_hidden                  = false
-    version                      = false
... (truncated)
hello-nf-core/solutions/core-hello-part2/subworkflows/local/utils_nfcore_hello_pipeline/main.nf
View 
@@ -8,13 +8,13 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { UTILS_NFSCHEMA_PLUGIN     } from '../../nf-core/utils_nfschema_plugin'
-include { paramsSummaryMap          } from 'plugin/nf-schema'
-include { samplesheetToList         } from 'plugin/nf-schema'
-include { paramsHelp                } from 'plugin/nf-schema'
-include { completionSummary         } from '../../nf-core/utils_nfcore_pipeline'
-include { UTILS_NFCORE_PIPELINE     } from '../../nf-core/utils_nfcore_pipeline'
-include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
+include { UTILS_NFSCHEMA_PLUGIN } from '../../nf-core/utils_nfschema_plugin'
+include { paramsSummaryMap } from 'plugin/nf-schema'
+include { samplesheetToList } from 'plugin/nf-schema'
+include { paramsHelp } from 'plugin/nf-schema'
... (truncated)
hello-nf-core/solutions/core-hello-part2/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
View 
@@ -10,9 +10,9 @@
 
 workflow UTILS_NEXTFLOW_PIPELINE {
     take:
-    print_version        // boolean: print version
-    dump_parameters      // boolean: dump parameters
-    outdir               //    path: base directory used to publish pipeline results
+    print_version // boolean: print version
+    dump_parameters // boolean: dump parameters
+    outdir //    path: base directory used to publish pipeline results
     check_conda_channels // boolean: check conda channels
 
     main:
@@ -72,10 +72,10 @@ def getWorkflowVersion() {
 //
... (truncated)
hello-nf-core/solutions/core-hello-part2/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
View 
@@ -1,9 +1,9 @@
 manifest {
-    name            = 'nextflow_workflow'
-    author          = """nf-core"""
-    homePage        = 'https://127.0.0.1'
-    description     = """Dummy pipeline"""
+    name = 'nextflow_workflow'
+    author = """nf-core"""
+    homePage = 'https://127.0.0.1'
+    description = """Dummy pipeline"""
     nextflowVersion = '!>=23.04.0'
-    version         = '9.9.9'
-    doi             = 'https://doi.org/10.5281/zenodo.5070524'
+    version = '9.9.9'
+    doi = 'https://doi.org/10.5281/zenodo.5070524'
... (truncated)
hello-nf-core/solutions/core-hello-part2/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
View 
@@ -125,12 +125,12 @@ def paramsSummaryMultiqc(summary_params) {
         }
 
     def yaml_file_text = "id: '${workflow.manifest.name.replace('/', '-')}-summary'\n" as String
-    yaml_file_text     += "description: ' - this information is collected when the pipeline is started.'\n"
-    yaml_file_text     += "section_name: '${workflow.manifest.name} Workflow Summary'\n"
-    yaml_file_text     += "section_href: 'https://github.com/${workflow.manifest.name}'\n"
-    yaml_file_text     += "plot_type: 'html'\n"
-    yaml_file_text     += "data: |\n"
-    yaml_file_text     += "${summary_section}"
+    yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n"
+    yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n"
+    yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n"
+    yaml_file_text += "plot_type: 'html'\n"
+    yaml_file_text += "data: |\n"
... (truncated)
hello-nf-core/solutions/core-hello-part2/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config(truncated)
hello-nf-core/solutions/core-hello-part2/subworkflows/nf-core/utils_nfschema_plugin/main.nf(truncated)
hello-nf-core/solutions/core-hello-part2/workflows/hello.nf(truncated)
hello-nf-core/solutions/core-hello-part3/conf/base.config(truncated)
hello-nf-core/solutions/core-hello-part3/conf/modules.config(truncated)
hello-nf-core/solutions/core-hello-part3/conf/test.config(truncated)
hello-nf-core/solutions/core-hello-part3/conf/test_full.config(truncated)
hello-nf-core/solutions/core-hello-part3/main.nf(truncated)
hello-nf-core/solutions/core-hello-part3/modules/local/collectGreetings.nf(truncated)
hello-nf-core/solutions/core-hello-part3/modules/local/convertToUpper.nf(truncated)
hello-nf-core/solutions/core-hello-part3/modules/local/cowpy.nf(truncated)
hello-nf-core/solutions/core-hello-part3/modules/local/sayHello.nf(truncated)
hello-nf-core/solutions/core-hello-part3/modules/nf-core/find/concatenate/main.nf(truncated)
hello-nf-core/solutions/core-hello-part3/nextflow.config(truncated)
hello-nf-core/solutions/core-hello-part3/subworkflows/local/utils_nfcore_hello_pipeline/main.nf(truncated)
hello-nf-core/solutions/core-hello-part3/subworkflows/nf-core/utils_nextflow_pipeline/main.nf(truncated)
hello-nf-core/solutions/core-hello-part3/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config(truncated)
hello-nf-core/solutions/core-hello-part3/subworkflows/nf-core/utils_nfcore_pipeline/main.nf(truncated)
hello-nf-core/solutions/core-hello-part3/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config(truncated)
hello-nf-core/solutions/core-hello-part3/subworkflows/nf-core/utils_nfschema_plugin/main.nf(truncated)
hello-nf-core/solutions/core-hello-part3/workflows/hello.nf(truncated)
hello-nf-core/solutions/core-hello-part4/conf/base.config(truncated)
hello-nf-core/solutions/core-hello-part4/conf/modules.config(truncated)
hello-nf-core/solutions/core-hello-part4/conf/test.config(truncated)
hello-nf-core/solutions/core-hello-part4/conf/test_full.config(truncated)
hello-nf-core/solutions/core-hello-part4/main.nf(truncated)
hello-nf-core/solutions/core-hello-part4/modules/local/collectGreetings.nf(truncated)
hello-nf-core/solutions/core-hello-part4/modules/local/convertToUpper.nf(truncated)
hello-nf-core/solutions/core-hello-part4/modules/local/cowpy.nf(truncated)
hello-nf-core/solutions/core-hello-part4/modules/local/cowpy/main.nf(truncated)
hello-nf-core/solutions/core-hello-part4/modules/local/sayHello.nf(truncated)
hello-nf-core/solutions/core-hello-part4/modules/nf-core/find/concatenate/main.nf(truncated)
hello-nf-core/solutions/core-hello-part4/nextflow.config(truncated)
hello-nf-core/solutions/core-hello-part4/subworkflows/local/utils_nfcore_hello_pipeline/main.nf(truncated)
hello-nf-core/solutions/core-hello-part4/subworkflows/nf-core/utils_nextflow_pipeline/main.nf(truncated)
hello-nf-core/solutions/core-hello-part4/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config(truncated)
hello-nf-core/solutions/core-hello-part4/subworkflows/nf-core/utils_nfcore_pipeline/main.nf(truncated)
hello-nf-core/solutions/core-hello-part4/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config(truncated)
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vdauwera and others added 19 commits May 8, 2026 17:48
@vdauwera
Improve Seqera platform part
c213df0
@vdauwera @claude
Add nextflow-triathlon working directory and rewrite Part 1 docs
40cc7d0 
Adds the complete nextflow-triathlon/ working directory with scripts
(1-hello.nf, 2-inputs.nf, main.nf), modules, data files, nextflow.config,
and a solutions/ subdirectory with symlinks for self-contained testing.

Rewrites 01_run_basics.md into four sections: Hello World, Process multiple
inputs, Run a multi-step pipeline, and Configure the pipeline. The config
section introduces nextflow.config structure and profiles, setting learners
up for the nf-core pipeline demo in Part 2.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@vdauwera @claude
Split nextflow-triathlon into basics/ and nf-core/ subdirectories
9fcc3f7 
Part 1 exercises now live under nextflow-triathlon/basics/, and Parts 2/3
nf-core runs use nextflow-triathlon/nf-core/. This prevents the triathlon
nextflow.config from overriding params.input when running nf-core pipelines
from the same directory.

Also adds laptop.config (withLabel overrides capping memory to 6 GB) for
local development, and updates rnaseq docs to reflect the current pipeline
version (3.26.0, revision e7ca46272c).

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@vdauwera @claude
Restructure Section 4 to show memory error and laptop.config fix
fa08bc9 
Rewrite sections 4.2 and 4.3 to:
- Show the memory failure when running rnaseq without config overrides
- Explain nf-core process labels and the withLabel: fix via laptop.config
- Transition to Seqera Platform as the path to real-scale analysis
- Add link to Seqera academic program

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@vdauwera @claude
Rename section 4.3 heading and remove stray run artifacts
2730bde 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@vdauwera @claude
Fix tutorial docs and config after walkthrough testing
ab4e10b 
- Comment out withName: 'cowpy' block in nextflow.config to prevent
  selector warning when running scripts without the cowpy process
- Add -with-report section and executor note to 01_run_basics.md
- Fix inline code formatting in headings (work/, -resume)
- Update nf-core/demo pull revision hash and directory listing in 02_run_nfcore.md
- Remove solutions/ directory from basics/ (not needed for this tutorial)

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@vdauwera @claude
Rewrite Part 3 Seqera Platform section with getting-started content a…
a88f546 
…nd CLI-first workflow

- Add section 1: sign up, Community Showcase, compute options (own infra vs Seqera Compute)
- Simplify section 2 launch form with test profile pre-filled; fold form details into info admonition
- Add tw CLI install instructions; fix tw launch to use workspace pipeline name
- Restructure section 4 as CLI-first: tw pipelines add, verify in Launchpad, then launch

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@vdauwera @claude
Add tw CLI setup with seqera config file and address remaining TODOs
d7f9b68 
- Add .seqera_config stub with comments pointing to where values are found in Seqera UI
- Rewrite section 3.3 to use config file for token and workspace ID
- Add tw --version expected output and recap sentence
- Add tip about TOWER_COMPUTE_ENV and link to tw CLI reference docs
- Add recap sentences after tw runs list and tw pipelines add outputs
- Fix .seqera_config path consistency throughout

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@vdauwera @claude
Rename nextflow-triathlon directory to triathlon
9697dc3 
Update all path references in orientation, Part 1, Part 2, and Part 3 docs.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@vdauwera @claude
Comment out unfinished video section in triathlon index
582dcce 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@vdauwera @claude
Rename 01_run_basics.md to 01_run_nextflow.md
f87287e 
Update references in mkdocs.yml, index.md, and 00_orientation.md.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@vdauwera @claude
Rename 03_seqera_platform.md to 03_run_seqera.md
1b915b9 
Update references in mkdocs.yml and index.md.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@vdauwera @claude
Address remaining TODOs across triathlon course
aa62363 
- Part 1: add output block code snippet and recap sentence; fold nextflow.config into collapsed admonition
- Part 2: replace sections 3.1.3-3.1.4 with brief validation note; fold laptop.config into collapsed admonition
- Part 3: address tw --version output, compute env tip, and workspace recap TODOs
- index.md: comment out unfinished video section

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@vdauwera @claude
Fix missing additional_information marker in triathlon index.md
dea3f99 
The index_page template requires a <!-- additional_information --> marker
to split summary content from course overview. Its absence caused the
Netlify build to error out.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@vdauwera @claude
Improve Part 1 and Part 2 content and exercises
84533fe 
- Part 1: add -ansi-log false run to show per-call output; fix output
  block in 1.4.4 to show 1-hello.nf; update main.nf publish paths from
  'main' to 'full_pipeline'; fix nextflow.config admonition type
- Part 2: rewrite 4.2 memory error explanation with base.config context;
  improve 3.2.1/3.2.2 with touch/run instructions, command output
  admonitions, and -resume flag; add .command.sh admonition for ext.args;
  replace ls with tree for conf/ listing; fix laptop.config admonition
  type; convert TODO to tip admonition for academic program

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@vdauwera @claude
Fix outputs, hashes, highlights and add tw params-file section across…
b5d5f16 
… triathlon Parts 1-3

Part 1 (01_run_nextflow.md):
- Fix output filename (Hello World!-output.txt, not Hello-output.txt)
- Update all console output hashes and revision IDs to match actual runs
- Fix section 1.4.4 output block (was showing main.nf instead of 1-hello.nf)
- Fix duplicate section 2.1 numbering (renumber to 2.1-2.4)
- Fix resume command typo (csv-resume → csv -resume) and remove stray -ansi-log false
- Add hl_lines to process output blocks, channel construction, container directive, and chaining

Part 2 (02_run_nfcore.md):
- Fix nf-core/demo asset tree path (pipelines/ → /workspaces/.nextflow/assets/)

Part 3 (03_run_seqera.md):
- Add explanation in 4.2 that input/outdir appear red (required, no defaults)
- Rewrite 4.3 as web interface launch with manual parameter entry
- Add new 4.4: CLI launch using -p test + --params-file for outdir
- Explain why tw launch requires --params-file instead of individual flags
- Update intro and summary to reflect two-path launch approach

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@vdauwera
Update survey link
0067a23
@vdauwera @claude
Restructure orientation and part tips to use triathlon/ as VSCode root
6c529d2 
- Replace "Course structure" with "Get ready to work" section matching other courses
- Set working directory to triathlon/ + code . to focus VSCode
- Add tree output showing full triathlon/ structure including .seqera_config
- Simplify Part 1 tip to relative cd basics
- Update Part 2 tip to include relative cd ../nf-core option

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@vdauwera @claude
Show how to bake params-file and profile into tw pipelines add
944fac5 
Update tip in section 4.4 to demonstrate passing --params-file and
--profile to tw pipelines add, so defaults are saved with the pipeline
registration rather than specified at launch time.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@edmundmiller edmundmiller mentioned this pull request May 16, 2026
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