nextflow-io · nvnieuwk · May 12, 2025 · May 12, 2025 · May 12, 2025 · May 12, 2025
diff --git a/docs/nextflow_schema/nextflow_schema_examples.md b/docs/nextflow_schema/nextflow_schema_examples.md
@@ -18,3 +18,5 @@ It is used as a test fixture in the nf-schema package [here](https://github.com/
 ```json
 --8<-- "src/testResources/nextflow_schema.json"
 ```
+
+Even more examples can be found in the plugin [`examples` directory](../../examples) in the GitHub repository.
diff --git a/docs/nextflow_schema/sample_sheet_schema_examples.md b/docs/nextflow_schema/sample_sheet_schema_examples.md
@@ -9,15 +9,6 @@ description: Example JSON Schema for a Nextflow pipeline `nextflow_schema.json`
 The nf-core/rnaseq pipeline was one of the first to have a sample sheet schema.
 You can see this, used for validating sample sheets with `--input` here: [`assets/schema_input.json`](https://github.com/nf-core/rnaseq/blob/5671b65af97fe78a2f9b4d05d850304918b1b86e/assets/schema_input.json).
 
-!!! tip
-
-    Note the approach used for validating filenames in the `fastq_2` column.
-    The column is optional, so if a `pattern` was supplied by itself then validation would fail
-    when no string is supplied.
-
-    Instead, we say that the string must _either_ match that pattern or it must have a
-    `maxLength` of `0` (an empty string).
-
 ```json
 {
   "$schema": "https://json-schema.org/draft/2020-12/schema",
@@ -71,3 +62,5 @@ It is used as a test fixture in the nf-schema package [here](https://github.com/
 ```json
 --8<-- "src/testResources/schema_input.json"
 ```
+
+Even more examples can be found in the plugin [`examples` directory](../../examples) in the GitHub repository.
diff --git a/examples/README.md b/examples/README.md
@@ -0,0 +1,13 @@
+# nf-schema examples
+
+This directory contains example files for the nf-schema project.
+
+1. [Help Message](./helpMessage/) contains a pipeline that generates a help message for a given schema.
+2. [Parameter summary log](./paramSummaryLog/) contains a pipeline that generates a summary log of the parameters used in a given schema.
+3. [Parameter summary map](./paramSummaryMap/) contains a pipeline that generates a summary map of the parameters used in a given schema. The difference between with the previous example is that this one produces a machine readable data structure instead of a human readable output string.
+4. [Basic samplesheet conversion](./samplesheetToListBasic/) contains a pipeline that converts a samplesheet to a list that can be easily converted to a channel for usage in the pipeline.
+5. [Samplesheet conversion with meta](./samplesheetToListMeta/) contains a pipeline that converts a samplesheet to a list that can be easily converted to a channel for usage in the pipeline. This example contains a meta map.
+6. [Samplesheet conversion order](./samplesheetToListOrder/) contains a pipeline that converts a samplesheet to a list. This example is used to explain the order of the fields in the samplesheet can be changed freely while maintaining the same output list order. The output order is based on the order of the fields in the schema.
+7. [Validate Parameters](./validateParameters/) contains a pipeline that validates the parameters used in a given schema.
+8. [Fail unrecognized parameters](./failUnrecognizedParameters/) contains a pipeline that fails when unrecognized parameters are used in a given schema.
+9. [Warning unrecognized parameters](./warningUnrecognizedParameters/) contains a pipeline that warns when unrecognized parameters are used in a given schema.
diff --git a/examples/helpMessage/README.md b/examples/helpMessage/README.md
@@ -0,0 +1,7 @@
+# Help Message
+
+This example demonstrates how to generate a help message for a given schema using the nf-schema plugin.
+
+There are two example log files provided in this directory:
+- `log.txt`: This log file shows the output when running the pipeline with the `--help` option. It contains the help message generated for the schema.
+- `log_outdir.txt`: This log file shows the output when running the pipeline with the `--help outdir` option. It contains the help message for the `outdir` parameter specifically.
diff --git a/examples/helpMessage/log.txt b/examples/helpMessage/log.txt
@@ -0,0 +1,25 @@
+
+ N E X T F L O W   ~  version 25.04.0
+
+Launching `pipeline/main.nf` [confident_lamarr] DSL2 - revision: 629cc11c05
+
+
+This is a help message for the pipeline.
+It provides information about the parameters and usage.
+
+    Typical pipeline command:
+
+  nextflow run my_pipeline --input input_file.csv
+
+--help         [boolean, string] Show the help message for all top level parameters. When a parameter is given to `--help`, the full help message of that parameter will be printed. 
+--helpFull     [boolean]         Show the help message for all non-hidden parameters. 
+--showHidden   [boolean]         Show all hidden parameters in the help message. This needs to be used in combination with `--help` or `--helpFull`. 
+
+Input/output options
+  --input      [string] Path to comma-separated file containing information about the samples in the experiment. 
+  --outdir     [string] The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure. 
+
+------------------------------------------------------
+
+For more information, please refer to the documentation.
+
diff --git a/examples/paramsHelp/log_outdir.txt → examples/helpMessage/log_outdir.txt b/examples/paramsHelp/log_outdir.txt → examples/helpMessage/log_outdir.txt
@@ -1,7 +1,13 @@
-N E X T F L O W  ~  version 23.04.1
-Launching `pipeline/main.nf` [exotic_rutherford] DSL2 - revision: 8bf4c8d053
 
-Typical pipeline command:
+ N E X T F L O W   ~  version 25.04.0
+
+Launching `pipeline/main.nf` [agitated_wegener] DSL2 - revision: 629cc11c05
+
+
+This is a help message for the pipeline.
+It provides information about the parameters and usage.
+
+    Typical pipeline command:
 
   nextflow run my_pipeline --input input_file.csv
 
@@ -10,3 +16,6 @@ Typical pipeline command:
     format     : directory-path
     description: The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
 ------------------------------------------------------
+
+For more information, please refer to the documentation.
+
diff --git a/examples/helpMessage/pipeline/main.nf b/examples/helpMessage/pipeline/main.nf
@@ -0,0 +1,3 @@
+workflow {
+
+}
diff --git a/examples/helpMessage/pipeline/nextflow.config b/examples/helpMessage/pipeline/nextflow.config
@@ -0,0 +1,23 @@
+plugins {
+  id '[email protected]'
+}
+
+params {
+  input = "samplesheet.csv"
+  outdir = "results"
+}
+
+validation {
+  help {
+    command = "nextflow run my_pipeline --input input_file.csv"
+    beforeText = """
+This is a help message for the pipeline.
+It provides information about the parameters and usage.
+
+    """
+    afterText = """
+For more information, please refer to the documentation.
+    """
+    enabled = true
+  }
+}
diff --git a/.../paramsHelp/pipeline/nextflow_schema.json → ...helpMessage/pipeline/nextflow_schema.json b/.../paramsHelp/pipeline/nextflow_schema.json → ...helpMessage/pipeline/nextflow_schema.json
diff --git a/examples/paramsHelp/log.txt b/examples/paramsHelp/log.txt
diff --git a/examples/paramsHelp/pipeline/main.nf b/examples/paramsHelp/pipeline/main.nf
diff --git a/examples/paramsHelp/pipeline/nextflow.config b/examples/paramsHelp/pipeline/nextflow.config
diff --git a/examples/paramsHelp/samplesheet.csv b/examples/paramsHelp/samplesheet.csv
diff --git a/examples/paramsSummaryLog/README.md b/examples/paramsSummaryLog/README.md
@@ -0,0 +1,6 @@
+# Parameters summary log
+
+This example demonstrates how to generate a summary log of the parameters used in a given schema using the nf-schema plugin.
+
+There's one example log file provided in this directory:
+- `log.txt`: This log file shows the output when running the pipeline.
diff --git a/examples/paramsSummaryLog/log.txt b/examples/paramsSummaryLog/log.txt
@@ -1,18 +1,24 @@
-N E X T F L O W  ~  version 23.04.1
-Launching `pipeline/main.nf` [sleepy_goldberg] DSL2 - revision: 7a280216f3
 
-Core Nextflow options
-  runName    : sleepy_goldberg
-  launchDir  : /Users/demo/GitHub/nextflow-io/nf-schema/examples/paramsSummaryLog
-  workDir    : /Users/demo/GitHub/nextflow-io/nf-schema/examples/paramsSummaryLog/work
-  projectDir : /Users/demo/GitHub/nextflow-io/nf-schema/examples/paramsSummaryLog/pipeline
-  userName   : demo
-  profile    : standard
-  configFiles:
+ N E X T F L O W   ~  version 25.04.0
+
+Launching `pipeline/main.nf` [angry_poitras] DSL2 - revision: fca518be2f
+
 
-Input/output options
+This is a summary message for the pipeline parameters.
+    Input/output options
   input      : samplesheet.csv
   outdir     : results
 
+Core Nextflow options
+  runName    : angry_poitras
+  launchDir  : /home/nvnieuwk/Documents/nextflow/nf-schema/examples/paramsSummaryLog
+  workDir    : /home/nvnieuwk/Documents/nextflow/nf-schema/examples/paramsSummaryLog/work
+  projectDir : /home/nvnieuwk/Documents/nextflow/nf-schema/examples/paramsSummaryLog/pipeline
+  userName   : nvnieuwk
+  profile    : standard
+  configFiles: /home/nvnieuwk/.nextflow/config, /home/nvnieuwk/Documents/nextflow/nf-schema/examples/paramsSummaryLog/pipeline/nextflow.config
+
 !! Only displaying parameters that differ from the pipeline defaults !!
 ------------------------------------------------------
+For more information, please refer to the documentation.
+
diff --git a/examples/paramsSummaryLog/pipeline/main.nf b/examples/paramsSummaryLog/pipeline/main.nf
@@ -1,3 +1,5 @@
 include { paramsSummaryLog } from 'plugin/nf-schema'
 
-log.info paramsSummaryLog(workflow)
+workflow {
+    log.info paramsSummaryLog(workflow)
+}
diff --git a/examples/paramsSummaryLog/pipeline/nextflow.config b/examples/paramsSummaryLog/pipeline/nextflow.config
@@ -1,8 +1,19 @@
 plugins {
-  id 'nf-schema@2.0.0'
+  id 'nf-schema@2.5.0'
 }
 
 params {
   input = "samplesheet.csv"
   outdir = "results"
 }
+
+validation {
+  summary {
+    beforeText = """
+This is a summary message for the pipeline parameters.
+    """
+    afterText = """
+For more information, please refer to the documentation.
+    """
+  }
+}
diff --git a/examples/paramsSummaryLog/samplesheet.csv b/examples/paramsSummaryLog/samplesheet.csv
diff --git a/examples/paramsSummaryMap/README.md b/examples/paramsSummaryMap/README.md
@@ -0,0 +1,6 @@
+# Parameters summary map
+
+This example demonstrates how to generate a summary map of the parameters used in a given schema using the nf-schema plugin.
+
+There's one example log file provided in this directory:
+- `log.txt`: This log file shows the output when running the pipeline, which prints out the parameters summary map.
diff --git a/examples/paramsSummaryMap/log.txt b/examples/paramsSummaryMap/log.txt
@@ -1,4 +1,6 @@
-N E X T F L O W  ~  version 23.04.1
-Launching `pipeline/main.nf` [happy_lamport] DSL2 - revision: c45338cd96
 
-[Core Nextflow options:[runName:happy_lamport, launchDir:/Users/ewels/GitHub/nextflow-io/nf-schema/examples/paramsSummaryMap, workDir:/Users/ewels/GitHub/nextflow-io/nf-schema/examples/paramsSummaryMap/work, projectDir:/Users/ewels/GitHub/nextflow-io/nf-schema/examples/paramsSummaryMap/pipeline, userName:ewels, profile:standard, configFiles:], Input/output options:[input:samplesheet.csv, outdir:results]]
+ N E X T F L O W   ~  version 25.04.0
+
+Launching `pipeline/main.nf` [irreverent_stallman] DSL2 - revision: 8bb467530c
+
+[Input/output options:[input:samplesheet.csv, outdir:results], Core Nextflow options:[runName:irreverent_stallman, launchDir:/home/nvnieuwk/Documents/nextflow/nf-schema/examples/paramsSummaryMap, workDir:/home/nvnieuwk/Documents/nextflow/nf-schema/examples/paramsSummaryMap/work, projectDir:/home/nvnieuwk/Documents/nextflow/nf-schema/examples/paramsSummaryMap/pipeline, userName:nvnieuwk, profile:standard, configFiles:/home/nvnieuwk/.nextflow/config, /home/nvnieuwk/Documents/nextflow/nf-schema/examples/paramsSummaryMap/pipeline/nextflow.config]]
diff --git a/examples/paramsSummaryMap/pipeline/main.nf b/examples/paramsSummaryMap/pipeline/main.nf
@@ -1,3 +1,5 @@
 include { paramsSummaryMap } from 'plugin/nf-schema'
 
-println paramsSummaryMap(workflow)
+workflow {
+    println paramsSummaryMap(workflow)
+}
diff --git a/examples/paramsSummaryMap/pipeline/nextflow.config b/examples/paramsSummaryMap/pipeline/nextflow.config
@@ -1,5 +1,5 @@
 plugins {
-  id 'nf-schema@2.0.0'
+  id 'nf-schema@2.5.0'
 }
 
 params {

diff --git a/examples/paramsSummaryMap/samplesheet.csv b/examples/paramsSummaryMap/samplesheet.csv
diff --git a/examples/samplesheetToListBasic/README.md b/examples/samplesheetToListBasic/README.md
@@ -0,0 +1,6 @@
+# Basic samplesheet conversion
+
+This example shows how to convert a samplesheet to a list that can be easily converted to a channel for usage in the pipeline.
+
+There's one example log file provided in this directory:
+- `log.txt`: This log file shows the output when running the pipeline, which prints out the samplesheet converted to a channel from a list.
diff --git a/examples/samplesheetToListBasic/launch.sh b/examples/samplesheetToListBasic/launch.sh
diff --git a/examples/samplesheetToListBasic/log.txt b/examples/samplesheetToListBasic/log.txt
@@ -1,4 +1,7 @@
-N E X T F L O W  ~  version 23.04.0
-Launching `pipeline/main.nf` [distraught_marconi] DSL2 - revision: 74f697a0d9
+
+ N E X T F L O W   ~  version 25.04.0
+
+Launching `pipeline/main.nf` [elated_almeida] DSL2 - revision: 34f1f7de6e
+
 [mysample1, input1_R1.fq.gz, input1_R2.fq.gz, forward]
 [mysample2, input2_R1.fq.gz, input2_R2.fq.gz, forward]
diff --git a/examples/samplesheetToListBasic/pipeline/main.nf b/examples/samplesheetToListBasic/pipeline/main.nf
@@ -1,5 +1,8 @@
 include { samplesheetToList } from 'plugin/nf-schema'
 
-ch_input = Channel.fromList(samplesheetToList(params.input, "assets/schema_input.json"))
+workflow {
+    ch_input = Channel.fromList(samplesheetToList(params.input, "assets/schema_input.json"))
+
+    ch_input.view()
+}
 
-ch_input.view()
diff --git a/examples/samplesheetToListBasic/pipeline/nextflow.config b/examples/samplesheetToListBasic/pipeline/nextflow.config
@@ -1,8 +1,8 @@
 plugins {
-  id 'nf-schema@2.0.0'
+  id 'nf-schema@2.5.0'
 }
 
 params {
-  input = "samplesheet.csv"
+  input = "${projectDir}/../samplesheet.csv"
   output = "results"
 }
diff --git a/examples/samplesheetToListMeta/README.md b/examples/samplesheetToListMeta/README.md
@@ -0,0 +1,6 @@
+# Samplesheet conversion with meta
+
+This example shows how to convert a samplesheet to a list that can be easily converted to a channel for usage in the pipeline. This example contains a meta map.
+
+There's one example log file provided in this directory:
+- `log.txt`: This log file shows the output when running the pipeline, which prints out the samplesheet converted to a channel from a list. This contains a meta map.
diff --git a/examples/samplesheetToListMeta/launch.sh b/examples/samplesheetToListMeta/launch.sh
diff --git a/examples/samplesheetToListMeta/log.txt b/examples/samplesheetToListMeta/log.txt
@@ -1,4 +1,7 @@
-N E X T F L O W  ~  version 23.04.0
-Launching `pipeline/main.nf` [romantic_kare] DSL2 - revision: 74f697a0d9
+
+ N E X T F L O W   ~  version 25.04.0
+
+Launching `pipeline/main.nf` [nostalgic_darwin] DSL2 - revision: 2d849659b1
+
 [[my_sample_id:mysample1, my_strandedness:forward], input1_R1.fq.gz, input1_R2.fq.gz]
 [[my_sample_id:mysample2, my_strandedness:forward], input2_R1.fq.gz, input2_R2.fq.gz]
diff --git a/examples/samplesheetToListMeta/pipeline/main.nf b/examples/samplesheetToListMeta/pipeline/main.nf
@@ -1,5 +1,7 @@
 include { samplesheetToList } from 'plugin/nf-schema'
 
-ch_input = Channel.fromList(samplesheetToList(params.input, "assets/schema_input.json"))
+workflow {
+    ch_input = Channel.fromList(samplesheetToList(params.input, "assets/schema_input.json"))
 
-ch_input.view()
+    ch_input.view()
+}
diff --git a/examples/samplesheetToListMeta/pipeline/nextflow.config b/examples/samplesheetToListMeta/pipeline/nextflow.config
@@ -1,8 +1,8 @@
 plugins {
-  id 'nf-schema@2.0.0'
+  id 'nf-schema@2.5.0'
 }
 
 params {
-  input = "samplesheet.csv"
+  input = "${projectDir}/../samplesheet.csv"
   output = "results"
 }
diff --git a/examples/samplesheetToListOrder/README.md b/examples/samplesheetToListOrder/README.md
@@ -0,0 +1,6 @@
+# Samplesheet conversion order
+
+This example shows how to convert a samplesheet to a list. This example is used to explain the order of the fields in the samplesheet can be changed freely while maintaining the same output list order. The output order is based on the order of the fields in the schema.
+
+There's one example log file provided in this directory:
+- `log.txt`: This log file shows the output when running the pipeline.
diff --git a/examples/samplesheetToListOrder/launch.sh b/examples/samplesheetToListOrder/launch.sh
diff --git a/examples/samplesheetToListOrder/log.txt b/examples/samplesheetToListOrder/log.txt
@@ -1,4 +1,7 @@
-N E X T F L O W  ~  version 23.04.0
-Launching `pipeline/main.nf` [elated_kowalevski] DSL2 - revision: 74f697a0d9
+
+ N E X T F L O W   ~  version 25.04.0
+
+Launching `pipeline/main.nf` [magical_wozniak] DSL2 - revision: 2d849659b1
+
 [forward, mysample1, input1_R2.fq.gz, input1_R1.fq.gz]
 [forward, mysample2, input2_R2.fq.gz, input2_R1.fq.gz]
diff --git a/examples/samplesheetToListOrder/pipeline/main.nf b/examples/samplesheetToListOrder/pipeline/main.nf
@@ -1,5 +1,7 @@
 include { samplesheetToList } from 'plugin/nf-schema'
 
-ch_input = Channel.fromList(samplesheetToList(params.input, "assets/schema_input.json"))
+workflow {
+    ch_input = Channel.fromList(samplesheetToList(params.input, "assets/schema_input.json"))
 
-ch_input.view()
+    ch_input.view()
+}
-Original file line number
+Diff line change
@@ Expand Up @@
     ```json
     --8<-- "src/testResources/nextflow_schema.json"
     ```
+    Even more examples can be found in the plugin [`examples` directory](../../examples) in the GitHub repository.