Add debugging side quest content (#639)

* Add debugging side quest content

* End of file fix

* Add periods to headings

* shorten intro

* Update docs/side_quests/debugging.md

* Update docs/side_quests/debugging.md

Co-authored-by: Adam Talbot <[email protected]>

* Update docs/side_quests/debugging.md

Co-authored-by: Adam Talbot <[email protected]>

* Update docs/side_quests/debugging.md

Co-authored-by: Adam Talbot <[email protected]>

* Update docs/side_quests/debugging.md

Co-authored-by: Adam Talbot <[email protected]>

* Update docs/side_quests/debugging.md

Co-authored-by: Adam Talbot <[email protected]>

* Apply suggestions from code review

Co-authored-by: Adam Talbot <[email protected]>

* remove duplication

* change to inputs

* add nextflow run and change order to invalid_process.nf

* add line highlighting, expand explanation

* add solution

* add nextflow run to bad_bash_var

* move into workflow

* propagate fixes into code

* suffle explanation to include run command, add collect

* expand on the value channel explanation

* add before after block

* call out to containers training

* Update docs/side_quests/debugging.md

Co-authored-by: Adam Talbot <[email protected]>

* note about syntax error

* have people add in stub themselves

* remove code commenting step

* note on host system error propagation

* simplify debugging journey by removing trace, report, timeline

* testing with nf-test

* linting

* fix formatting

* fix formatting

* Update docs/side_quests/debugging.md

* Update contents, trial before/ after type syntax for error

* Revert "Update contents, trial before/ after type syntax for error"

This reverts commit efcf91a.

* Update contents

* Reformat exercise

* try adding consistency

* Fixes down to bad_bash_var

* syntax fix

* Misc fixes and Nextflow versions

* Fix highlight

* Fix highlight

* Add incorrect_num_args screenshot

* Fix highlight

* Misc fixes

* Misc fixes

* Fix wording, highlight

* Update run message

* Turn on some line numberings to check it works

* Tidy up view() coverage

* More refinements

* formatting fix

* More fixes

* Tidy up stubs etc

* Last fixes before exercise

* Remove bug comment

* Fix debugging phases

* Fix exercise formatting

* Fix exercise formatting

* Try to finalise solution

* Fix formatting

* Move summary out of solution

* Prettier

* Fix listing

* Fix misc errors

* Add missing line nums

* Add process debugging techniques

* prettier

* Update docs/side_quests/debugging.md

* Update docs/side_quests/debugging.md

* Update docs/side_quests/debugging.md

* fix prettier linting

* reduce level of numbering to prevent autonumbering by the renderer

* numbering

* try indenting text further to fix numbering

* revert to using bold numbers

* Improve syntax debugging ending

---------

Co-authored-by: FriederikeHanssen <[email protected]>
Co-authored-by: Adam Talbot <[email protected]>

Author: 3 people

docs/side_quests/debugging.md

@@ -57,6 +57,7 @@ nav:
       - side_quests/ide_features.md
       - side_quests/workflows_of_workflows.md
       - side_quests/splitting_and_grouping.md
+      - side_quests/debugging.md
       - side_quests/nf-test.md
       - side_quests/nf-core.md
   - Fundamentals Training:

docs/side_quests/img/bad_syntax.png

@@ -0,0 +1,24 @@
+#!/usr/bin/env nextflow
+
+process PROCESS_FILES {
+    input:
+    val sample_name
+
+    output:
+    path "${sample_name}_output.txt"
+
+    script:
+    """
+    prefix="${sample_name}_output"
+    echo "Processing ${sample_name}" > ${prefix}.txt
+    """
+}
+
+workflow {
+
+    // Create input channel
+    input_ch = Channel.of('sample1', 'sample2', 'sample3')
+
+    // Call the process with the input channel
+    PROCESS_FILES(input_ch)
+}

docs/side_quests/img/incorrect_num_args.png

@@ -0,0 +1,24 @@
+#!/usr/bin/env nextflow
+
+process PROCESS_FILES {
+    input:
+    val sample_name
+
+    output:
+    path "${sample_name}_output.txt"
+
+    script:
+    """
+    echo "Processing ${sample_name}" > ${sample_name}_output.txt
+    """
+}
+
+workflow {
+
+    input_ch = Channel.of(
+        ['sample1', 'file1.txt'],
+        ['sample2', 'file2.txt'],
+        ['sample3', 'file3.txt'],
+    )
+    PROCESS_FILES(input_ch)
+}

docs/side_quests/img/invalid_process_message.png

@@ -0,0 +1,28 @@
+#!/usr/bin/env nextflow
+
+process PROCESS_FILES {
+    input:
+    val sample_name
+
+    output:
+    path "${sample_name}_output.txt"
+
+    script:
+    """
+    echo "Processing ${sample_name}" > ${sample_name}_output.txt
+    """
+}
+
+workflow {
+
+    input_ch = Channel.of(
+            ['sample1', 'file1.txt'],
+            ['sample2', 'file2.txt'],
+            ['sample3', 'file3.txt'],
+        )
+        .view { "Channel content: ${it}" }
+        .map { tuple -> tuple[0] }
+        .view { "After mapping: ${it}" }
+
+    PROCESS_FILES(input_ch)
+}

docs/side_quests/img/nonlethal.png

@@ -0,0 +1,31 @@
+#!/usr/bin/env nextflow
+
+process PROCESS_FILES {
+    debug true
+
+    input:
+    val sample_name
+
+    output:
+    path "${sample_name}_output.txt"
+
+    script:
+    """
+    echo "Sample name inside process is ${sample_name}"
+    echo "Processing ${sample_name}" > ${sample_name}_output.txt
+    """
+}
+
+workflow {
+
+    input_ch = Channel.of(
+            ['sample1', 'file1.txt'],
+            ['sample2', 'file2.txt'],
+            ['sample3', 'file3.txt'],
+        )
+        .view { "Channel content: ${it}" }
+        .map { tuple -> tuple[0] }
+        .view { "After mapping: ${it}" }
+
+    PROCESS_FILES(input_ch)
+}