Workflow outputs in Side Quests

docs/en/docs/side_quests/debugging/index.md

@@ -2415,7 +2415,7 @@ Now it's time to put the systematic debugging approach into practice. The workfl
         ```
         **Fix:** Take the output from the previous process
         ```groovy linenums="88"
-        handleFiles(heavyProcess.out)
+        file_ch = handleFiles(heavy_ch)
         ```
 
         With that, the whole workflow should run.
@@ -2439,7 +2439,6 @@ Now it's time to put the systematic debugging approach into practice. The workfl
         * Process with input/output mismatch
         */
         process processFiles {
-            publishDir "${params.output}/processed", mode: 'copy'
 
             input:
                 tuple val(sample_id), path(input_file)
@@ -2458,7 +2457,6 @@ Now it's time to put the systematic debugging approach into practice. The workfl
         * Process with resource issues
         */
         process heavyProcess {
-            publishDir "${params.output}/heavy", mode: 'copy'
 
             time '100 s'
 
@@ -2481,7 +2479,6 @@ Now it's time to put the systematic debugging approach into practice. The workfl
         * Process with file handling issues
         */
         process handleFiles {
-            publishDir "${params.output}/files", mode: 'copy'
 
             input:
                 path input_file
@@ -2501,7 +2498,7 @@ Now it's time to put the systematic debugging approach into practice. The workfl
         * Main workflow with channel issues
         */
         workflow {
-
+            main:
             // Channel with incorrect usage
             input_ch = channel
                 .fromPath(params.input)
@@ -2512,7 +2509,24 @@ Now it's time to put the systematic debugging approach into practice. The workfl
 
             heavy_ch = heavyProcess(input_ch.map{it[0]})
 
-            handleFiles(heavyProcess.out)
+            file_ch = handleFiles(heavy_ch)
+
+            publish:
+            processed = processed_ch
+            heavy = heavy_ch
+            files = file_ch
+        }
+
+        output {
+            processed {
+                path 'processed'
+            }
+            heavy {
+                path 'heavy'
+            }
+            files {
+                path 'files'
+            }
         }
         ```
 

docs/en/docs/side_quests/dev_environment/index.md

@@ -283,7 +283,6 @@ Efficient navigation is crucial when working with complex workflows spanning mul
     ```groovy title="basic_workflow.nf" linenums="3"
     process FASTQC {
         tag "${sample_id}"
-        publishDir "${params.output_dir}/fastqc", mode: 'copy'
 
         input:
         tuple val(sample_id), path(reads)
@@ -417,13 +416,13 @@ This is invaluable when:
 
 Sometimes you need to find where specific patterns are used across your entire project. Press `Ctrl/Cmd+Shift+F` to open the search panel.
 
-Try searching for `publishDir` across the workspace:
+Try searching for `container` across the workspace:
 
 ![Project search](img/project_search.png)
 
-This shows you every file that uses publish directories, helping you:
+This shows you every file that uses the container directive, helping you:
 
-- Understand output organization patterns
+- Understand which processes use containers
 - Find examples of specific directives
 - Ensure consistency across modules
 

docs/en/docs/side_quests/essential_scripting_patterns/index.md

@@ -896,7 +896,7 @@ Fix this by adding conditional logic to the `FASTP` process `script:` block. An
 
 === "After"
 
-    ```groovy title="main.nf" linenums="10" hl_lines="3-27"
+    ```groovy title="main.nf" linenums="10" hl_lines="2-26"
         script:
         // Simple single-end vs paired-end detection
         def is_single = reads instanceof List ? reads.size() == 1 : true
@@ -1001,8 +1001,6 @@ Take a look a the module file `modules/generate_report.nf`:
 ```groovy title="modules/generate_report.nf" linenums="1"
 process GENERATE_REPORT {
 
-    publishDir 'results/reports', mode: 'copy'
-
     input:
     tuple val(meta), path(reads)
 
@@ -1378,7 +1376,7 @@ cat work/48/6db0c9e9d8aa65e4bb4936cd3bd59e/.command.run | grep "docker run"
 You should see something like:
 
 ```bash title="docker command"
-    docker run -i --cpu-shares 4096 --memory 2048m -e "NXF_TASK_WORKDIR" -v /workspaces/training/side-quests/essential_scripting_patterns:/workspaces/training/side-quests/essential_scripting_patterns -w "$NXF_TASK_WORKDIR" --name $NXF_BOXID community.wave.seqera.io/library/fastp:0.24.0--62c97b06e8447690 /bin/bash -ue /workspaces/training/side-quests/essential_scripting_patterns/work/48/6db0c9e9d8aa65e4bb4936cd3bd59e/.command.sh
+    docker run -i --cpu-shares 2048 --memory 2048m -e "NXF_TASK_WORKDIR" -v /workspaces/training/side-quests/essential_scripting_patterns:/workspaces/training/side-quests/essential_scripting_patterns -w "$NXF_TASK_WORKDIR" --name $NXF_BOXID community.wave.seqera.io/library/fastp:0.24.0--62c97b06e8447690 /bin/bash -ue /workspaces/training/side-quests/essential_scripting_patterns/work/48/6db0c9e9d8aa65e4bb4936cd3bd59e/.command.sh
 ```
 
 In this example we've chosen an example that requested 2 CPUs (`--cpu-shares 2048`), because it was a high-depth sample, but you should see different CPU allocations depending on the sample depth. Try this for the other tasks as well.
@@ -1393,7 +1391,7 @@ Another powerful pattern is using `task.attempt` for retry strategies. To show w
     process FASTP {
         container 'community.wave.seqera.io/library/fastp:0.24.0--62c97b06e8447690'
 
-        cpus { meta.depth > 40000000 ? 4 : 2 }
+        cpus { meta.depth > 40000000 ? 2 : 1 }
         memory 1.GB
 
         input:
@@ -1406,7 +1404,7 @@ Another powerful pattern is using `task.attempt` for retry strategies. To show w
     process FASTP {
         container 'community.wave.seqera.io/library/fastp:0.24.0--62c97b06e8447690'
 
-        cpus { meta.depth > 40000000 ? 4 : 2 }
+        cpus { meta.depth > 40000000 ? 2 : 1 }
         memory 2.GB
 
         input:
@@ -1432,7 +1430,7 @@ nextflow run main.nf
       Detecting adapter sequence for read1...
       No adapter detected for read1
 
-      .command.sh: line 7:   101 Killed                  fastp --in1 SAMPLE_002_S2_L001_R1_001.fastq --out1 sample_002_trimmed.fastq.gz --json sample_002.fastp.json --html sample_002.fastp.html --thread 2
+      .command.sh: line 7:   101 Killed                  fastp --in1 SAMPLE_002_S2_L001_R1_001.fastq --out1 sample_002_trimmed.fastq.gz --json sample_002.fastp.json --html sample_002.fastp.html --thread 1
     ```
 
 This indicates that the process was killed for exceeding memory limits.
@@ -1447,7 +1445,7 @@ To make our workflow more robust, we can implement a retry strategy that increas
     process FASTP {
         container 'community.wave.seqera.io/library/fastp:0.24.0--62c97b06e8447690'
 
-        cpus { meta.depth > 40000000 ? 4 : 2 }
+        cpus { meta.depth > 40000000 ? 2 : 1 }
         memory { 1.GB * task.attempt }
         errorStrategy 'retry'
         maxRetries 2
@@ -1462,7 +1460,7 @@ To make our workflow more robust, we can implement a retry strategy that increas
     process FASTP {
         container 'community.wave.seqera.io/library/fastp:0.24.0--62c97b06e8447690'
 
-        cpus { meta.depth > 40000000 ? 4 : 2 }
+        cpus { meta.depth > 40000000 ? 2 : 1 }
         memory 2.GB
 
         input:

docs/en/docs/side_quests/metadata/index.md

@@ -133,9 +133,16 @@ Open the `main.nf` workflow file to examine the workflow stub we're giving you a
 #!/usr/bin/env nextflow
 
 workflow  {
-
+    main:
     ch_datasheet = channel.fromPath("./data/datasheet.csv")
 
+    publish:
+    cowpy_art = channel.empty()
+}
+
+output {
+    cowpy_art {
+    }
 }
 ```
 
@@ -151,24 +158,16 @@ Make the following changes to add a `splitCsv()` operation to the channel constr
 
 === "After"
 
-    ```groovy title="main.nf" linenums="3" hl_lines="4-5"
-    workflow  {
-
+    ```groovy title="main.nf" linenums="5" hl_lines="3-4"
         ch_datasheet = channel.fromPath("./data/datasheet.csv")
             .splitCsv(header: true)
             .view()
-
-    }
     ```
 
 === "Before"
 
-    ```groovy title="main.nf" linenums="3"
-    workflow  {
-
+    ```groovy title="main.nf" linenums="5"
         ch_datasheet = channel.fromPath("./data/datasheet.csv")
-
-    }
     ```
 
 Note that we're using the `header: true` option to tell Nextflow to read the first row of the CSV file as the header row.
@@ -254,29 +253,21 @@ Make the following edits to the workflow:
 
 === "After"
 
-    ```groovy title="main.nf" linenums="3" hl_lines="5-7"
-    workflow  {
-
+    ```groovy title="main.nf" linenums="5" hl_lines="4-6"
         ch_datasheet = channel.fromPath("./data/datasheet.csv")
             .splitCsv(header: true)
             .map{ row ->
                 row.character
             }
             .view()
-
-    }
     ```
 
 === "Before"
 
-    ```groovy title="main.nf" linenums="3"
-    workflow  {
-
+    ```groovy title="main.nf" linenums="5"
         ch_datasheet = channel.fromPath("./data/datasheet.csv")
             .splitCsv(header: true)
             .view()
-
-    }
     ```
 
 Now run the workflow again:
@@ -887,8 +878,6 @@ You can open the module file to examine its code:
 // Generate ASCII art with cowpy
 process COWPY {
 
-    publishDir "results/", mode: 'copy'
-
     container 'community.wave.seqera.io/library/cowpy:1.1.5--3db457ae1977a273'
 
     input:
@@ -1074,7 +1063,7 @@ This confirms we're able to access the file and the character for each element i
 
 #### 3.2.3. Call the `COWPY` process
 
-Now let's put it all together and actually call the `COWPY` process on the `ch_languages` channel.
+Now we can put it all together and actually call the `COWPY` process on the `ch_languages` channel.
 
 In the main workflow, make the following code changes:
 
@@ -1086,18 +1075,23 @@ In the main workflow, make the following code changes:
             ch_languages.map { meta, file -> file },
             ch_languages.map { meta, file -> meta.character }
         )
+
+        publish:
+        cowpy_art = COWPY.out
     ```
 
 === "Before"
 
     ```groovy title="main.nf" linenums="34"
         // Temporary: access the file and character
-        ch_languages.map { meta, file -> [file, meta.character] }
-            .view()
+        ch_languages.map { meta, file -> file }.view { file -> "File: " + file }
+        ch_languages.map { meta, file -> meta.character }.view { character -> "Character: " + character }
+
+        publish:
+        cowpy_art = channel.empty()
     ```
 
-You see we simply copy the two map operations (minus the `.view()` statements) as the inputs to the process call.
-Just make sure you don't forget the comma between them!
+We replaced the temporary view operations with the actual `COWPY` process call, and updated the `publish:` section to wire up `COWPY.out` for publishing.
 
 It's a bit clunky, but we'll see how to make that better in the next section.
 
@@ -1270,18 +1264,24 @@ Make the following edits to the main workflow:
 === "After"
 
     ```groovy title="main.nf" linenums="34" hl_lines="2"
-    // Run cowpy to generate ASCII art
-    COWPY(ch_languages)
+        // Run cowpy to generate ASCII art
+        COWPY(ch_languages)
+
+        publish:
+        cowpy_art = COWPY.out
     ```
 
 === "Before"
 
     ```groovy title="main.nf" linenums="34" hl_lines="3-4"
-    // Run cowpy to generate ASCII art
-    COWPY(
-        ch_languages.map { meta, file -> file },
-        ch_languages.map { meta, file -> meta.character }
-    )
+        // Run cowpy to generate ASCII art
+        COWPY(
+            ch_languages.map { meta, file -> file },
+            ch_languages.map { meta, file -> meta.character }
+        )
+
+        publish:
+        cowpy_art = COWPY.out
     ```
 
 That simplifies the call significantly!

docs/en/docs/side_quests/nf_test/index.md

@@ -119,8 +119,6 @@ You can see the full workflow code below.
     */
     process sayHello {
 
-        publishDir 'results', mode: 'copy'
-
         input:
             val greeting
 
@@ -138,8 +136,6 @@ You can see the full workflow code below.
     */
     process convertToUpper {
 
-        publishDir 'results', mode: 'copy'
-
         input:
             path input_file
 
@@ -153,7 +149,7 @@ You can see the full workflow code below.
     }
 
     workflow {
-
+        main:
         // create a channel for inputs from a CSV file
         greeting_ch = channel.fromPath(params.input_file).splitCsv().flatten()
 
@@ -162,6 +158,17 @@ You can see the full workflow code below.
 
         // convert the greeting to uppercase
         convertToUpper(sayHello.out)
+
+        publish:
+        greetings = sayHello.out
+        upper_greetings = convertToUpper.out
+    }
+
+    output {
+        greetings {
+        }
+        upper_greetings {
+        }
     }
     ```