Merge pull request #541 from nextflow-io/workflows_of_workflows

Add workflows of workflows side quest

Author: pinin4fjords

docs/side_quests/workflows_of_workflows.md

@@ -1 +1,8 @@
-// This main.nf script has intentionally been left blank to run on Seqera Platform
+include { GREETING_WORKFLOW } from './workflows/greeting'
+
+workflow {
+    Channel.from('Alice', 'Bob', 'Charlie') | GREETING_WORKFLOW
+
+    GREETING_WORKFLOW.out.greetings_ch.view { "Original: $it" }
+    GREETING_WORKFLOW.out.timestamped_ch.view { "Timestamped: $it" }
+}

main.nf

@@ -20,6 +20,7 @@ nav:
       - hello_nextflow/06_hello_config.md
   - Side Quests:
       - side_quests/nf-test.md
+      - side_quests/workflows_of_workflows.md
       - hello_nextflow/survey.md
       - hello_nextflow/next_steps.md
   - Nextflow for Genomics:
@@ -189,6 +190,7 @@ plugins:
         - advanced/index.md
         - advanced/orientation.md
         - side_quests/nf-test.md
+        - side_quests/workflows_of_workflows.md
         - nf4_science/genomics/03_modules.md
         - nf4_science/genomics/04_testing.md
 

mkdocs.yml

@@ -0,0 +1,16 @@
+include { GREETING_WORKFLOW } from './workflows/greeting'
+include { TRANSFORM_WORKFLOW } from './workflows/transform'
+
+workflow {
+    names = Channel.from('Alice', 'Bob', 'Charlie')
+
+    // Run the greeting workflow
+    GREETING_WORKFLOW(names)
+
+    // Run the transform workflow
+    TRANSFORM_WORKFLOW(GREETING_WORKFLOW.out.timestamped)
+
+    // View results
+    TRANSFORM_WORKFLOW.out.upper.view { "Uppercase: $it" }
+    TRANSFORM_WORKFLOW.out.reversed.view { "Reversed: $it" }
+}

side-quests/solutions/workflows_of_workflows/main.nf

@@ -0,0 +1,18 @@
+include { VALIDATE_NAME } from '../modules/validate_name'
+include { SAY_HELLO } from '../modules/say_hello'
+include { TIMESTAMP_GREETING } from '../modules/timestamp_greeting'
+
+workflow GREETING_WORKFLOW {
+    take:
+        names_ch        // Input channel with names
+
+    main:
+        // Chain processes: validate -> create greeting -> add timestamp
+        validated_ch = VALIDATE_NAME(names_ch)
+        greetings_ch = SAY_HELLO(validated_ch)
+        timestamped_ch = TIMESTAMP_GREETING(greetings_ch)
+
+    emit:
+        greetings = greetings_ch      // Original greetings
+        timestamped = timestamped_ch  // Timestamped greetings
+}

side-quests/solutions/workflows_of_workflows/workflows/greeting.nf

@@ -0,0 +1,16 @@
+include { SAY_HELLO_UPPER } from '../modules/say_hello_upper'
+include { REVERSE_TEXT } from '../modules/reverse_text'
+
+workflow TRANSFORM_WORKFLOW {
+    take:
+        input_ch         // Input channel with messages
+
+    main:
+        // Apply transformations in sequence
+        upper_ch = SAY_HELLO_UPPER(input_ch)
+        reversed_ch = REVERSE_TEXT(upper_ch)
+
+    emit:
+        upper = upper_ch        // Uppercase greetings
+        reversed = reversed_ch  // Reversed uppercase greetings
+}

side-quests/solutions/workflows_of_workflows/workflows/transform.nf

@@ -0,0 +1,19 @@
+/*
+ * Use a text manipulation tool to reverse the text in a file
+ */
+process REVERSE_TEXT {
+    publishDir 'results', mode: 'copy'
+
+    tag "reversing ${input_file}"
+
+    input:
+        path input_file
+
+    output:
+        path "REVERSED-${input_file}"
+
+    script:
+    """
+    cat '${input_file}' | rev > 'REVERSED-${input_file}'
+    """
+}

side-quests/workflows_of_workflows/modules/reverse_text.nf

@@ -0,0 +1,21 @@
+#!/usr/bin/env nextflow
+
+/*
+ * Use echo to print 'Hello World!' to a file
+ */
+process SAY_HELLO {
+    publishDir 'results', mode: 'copy'
+
+    tag "greeting ${name}"
+
+    input:
+    val name
+
+    output:
+    path "${name}-output.txt"
+
+    script:
+    """
+    echo 'Hello, ${name}!' > "${name}-output.txt"
+    """
+}

side-quests/workflows_of_workflows/modules/say_hello.nf

@@ -0,0 +1,21 @@
+#!/usr/bin/env nextflow
+
+/*
+ * Use a text replacement tool to convert the greeting to uppercase
+ */
+process SAY_HELLO_UPPER {
+    publishDir 'results', mode: 'copy'
+
+    tag "converting ${input_file}"
+
+    input:
+        path input_file
+
+    output:
+        path "UPPER-${input_file}"
+
+    script:
+    """
+    cat '${input_file}' | tr '[a-z]' '[A-Z]' > 'UPPER-${input_file}'
+    """
+}

side-quests/workflows_of_workflows/modules/say_hello_upper.nf

@@ -0,0 +1,15 @@
+process TIMESTAMP_GREETING {
+    tag "adding timestamp to greeting"
+
+    input:
+    path greeting_file
+
+    output:
+    path 'timestamped_*.txt'
+
+    script:
+    def base_name = greeting_file.baseName
+    """
+    echo "[\$(date '+%Y-%m-%d %H:%M:%S')] \$(cat $greeting_file)" > timestamped_${base_name}.txt
+    """
+}