Add Seqera Platform Automation side quest by adamrtalbot · Pull Request #968 · nextflow-io/training

adamrtalbot · 2026-06-16T17:06:38Z

Summary

Adds a new Seqera Platform Automation side quest that walks the Platform's programmatic surface across three workspace roles of decreasing privilege (Admin → Maintain → Launch), each handing an artifact to the next.

Lesson: docs/en/docs/side_quests/platform_automation/index.md — create compute environments (Batch Forge UI + Terraform), add pipelines to the Launchpad four ways (UI, tw, seqerakit, Terraform), and launch (GUI, tw, seqerakit, Actions). The throughline is declarative existence (Terraform) vs imperative actions (UI, tw, seqerakit).
Runnable assets: side-quests/platform_automation/ — terraform/compute-env/, terraform/pipeline/, and seqerakit/ with *.tfvars.example templates.
Devcontainer: adds Terraform (hashicorp.terraform extension), tw (0.32.0), and seqerakit (0.5.7) to the toolchain.

Notes

The page is intentionally not wired into the nav / side_quests/index.md table in this PR.
The "What's next?" link points at the Building with Seqera AI (CoScientist) side quest, which lands in [ DO NOT MERGE ] Side quest/co scientist #963. The relative link target only resolves once [ DO NOT MERGE ] Side quest/co scientist #963 merges — worth coordinating merge order.

Verification

uv run .github/check_headings.py docs/en/docs/side_quests/platform_automation/index.md → 0 errors
npx prettier --check on the lesson → passes
git check-ignore confirms terraform.tfvars/*.tfstate are ignored while *.tfvars.example stay tracked

Generated by Claude Code

Port the Platform Automation training module from the standalone m42-platform-advanced-training repo into the training collection as a single-page side quest, following the side_quests convention. - docs/en/docs/side_quests/platform_automation/index.md: the guide, with codespace badge, asset paths, and cd commands retargeted to nextflow-io/training and side-quests/platform_automation/. - side-quests/platform_automation/{terraform,seqerakit}: the Terraform (compute-env, pipeline) and seqerakit assets, verbatim aside from path/reference fixes and repaired code fences in the seqerakit README. - .editorconfig: add 2-space rule for *.tf/*.tfvars (terraform fmt style). Intentionally not added to the mkdocs nav or the side_quests index table. Passes pre-commit (prettier, editorconfig, whitespace, eof), the heading checker, terraform validate, and a non-strict mkdocs build. Generated by Claude Code

The platform_automation side quest needs Terraform, the Seqera CLI (tw), and seqerakit. Add them to the dev image the same way the rest of the toolchain is managed (features baked into the codespaces-dev/local-dev image), not via setup.sh: - terraform: official devcontainers/features/terraform feature, pinned to 1.9.8 with tflint/terragrunt disabled. - tw: new local-features/seqera-cli feature, mirroring tower-agent but arch-aware (x86_64/arm64) so the multi-arch image build stays green. - seqerakit: added to the existing uv-tools feature (pure-Python uv tool). - hashicorp.terraform VS Code extension added to all three configs. The tools land in the prebuilt image once docker-devcontainer rebuilds on merge to master; the production devcontainer pulls that image. Generated by Claude Code

The assets moved from the repo root into side-quests/platform_automation/, so the root-relative `cd` commands broke mid-sequence: after cd-ing into terraform/compute-env, a later `cd side-quests/platform_automation/seqerakit` fails. Make every `cd` absolute (/workspaces/training/...) so each step works from wherever the previous one left the learner, matching the absolute-path convention used elsewhere in the side quests. Also drop the stale "ends with 'Toolchain ready'" line: that string came from the standalone repo's setup.sh and is not printed by the training devcontainer. Generated by Claude Code

…st next step Add Terraform ignore rules so learner-generated terraform.tfvars and *.tfstate (both contain Azure credentials) are not committed; the committed *.tfvars.example files stay tracked. Point the "What's next?" cross-reference at the in-site Building with Seqera AI (CoScientist) side quest instead of a generic GitHub link. Generated by Claude Code

netlify · 2026-06-16T17:06:46Z

✅ Deploy Preview for nextflow-training ready!

Name	Link
🔨 Latest commit	`9e8dc32`
🔍 Latest deploy log	https://app.netlify.com/projects/nextflow-training/deploys/6a32dead0ba30b0008ca61c0
😎 Deploy Preview	https://deploy-preview-968--nextflow-training.netlify.app
📱 Preview on mobile	Toggle QR Code... Use your smartphone camera to open QR code link.

To edit notification comments on pull requests, go to your Netlify project configuration.

github-actions · 2026-06-16T17:07:49Z

Nextflow linting complete!

⚠️ 35 files had 70 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 70 issues

Type	Location	Message
Warning	hello-nf-core/solutions/composable-hello/hello.nf:36:5	Emit name should be omitted when there is only one emit
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_nextflow_pipeline/main.nf:43:5	Emit name should be omitted when there is only one emit
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/subworkflows/nf-core/utils_nfcore_pipeline/main.nf:20:5	Emit name should be omitted when there is only one emit
Warning	hello-nf-core/solutions/core-hello-part2/subworkflows/nf-core/utils_nfschema_plugin/main.nf:72:5	Emit name should be omitted when there is only one emit
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_nextflow_pipeline/main.nf:43:5	Emit name should be omitted when there is only one emit
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/subworkflows/nf-core/utils_nfcore_pipeline/main.nf:20:5	Emit name should be omitted when there is only one emit
Warning	hello-nf-core/solutions/core-hello-part3/subworkflows/nf-core/utils_nfschema_plugin/main.nf:72:5	Emit name should be omitted when there is only one emit
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_nextflow_pipeline/main.nf:43:5	Emit name should be omitted when there is only one emit
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/subworkflows/nf-core/utils_nfcore_pipeline/main.nf:20:5	Emit name should be omitted when there is only one emit
Warning	hello-nf-core/solutions/core-hello-part4/subworkflows/nf-core/utils_nfschema_plugin/main.nf:72:5	Emit name should be omitted when there is only one emit
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_nextflow_pipeline/main.nf:43:5	Emit name should be omitted when there is only one emit
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/subworkflows/nf-core/utils_nfcore_pipeline/main.nf:20:5	Emit name should be omitted when there is only one emit
Warning	hello-nf-core/solutions/core-hello-part5/subworkflows/nf-core/utils_nfschema_plugin/main.nf:72:5	Emit name should be omitted when there is only one emit
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_nextflow_pipeline/main.nf:43:5	Emit name should be omitted when there is only one emit
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/subworkflows/nf-core/utils_nfcore_pipeline/main.nf:20:5	Emit name should be omitted when there is only one emit
Warning	hello-nf-core/solutions/core-hello-start/subworkflows/nf-core/utils_nfschema_plugin/main.nf:44:5	Emit name should be omitted when there is only one emit
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	hello-nf-core/solutions/core-hello-start/workflows/hello.nf:54:5	Emit name should be omitted when there is only one emit
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

File	Diff
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)
hello-nf-core/solutions/core-hello-part4/subworkflows/nf-core/utils_nfschema_plugin/main.nf	(truncated)
hello-nf-core/solutions/core-hello-part4/workflows/hello.nf	(truncated)
hello-nf-core/solutions/core-hello-part5/conf/base.config	(truncated)
hello-nf-core/solutions/core-hello-part5/conf/modules.config	(truncated)
hello-nf-core/solutions/core-hello-part5/conf/test.config	(truncated)

tower-cli publishes no tw-linux-arm64 asset, so the multi-arch image build 404'd on the arm64 leg. Keep the native binary on x86_64 and fall back to the arch-independent tw-jar.jar (run via Java) on arm64. Generated by Claude Code

Section 0 jumped from opening the Codespace straight to creating a token, never walking participants into the working directory or showing its contents. Add "Move into the project directory" (cd + code .) and "Review the materials" (directory tree) subsections, matching the debugging side quest pattern. Generated by Claude Code

… workshop handle Review pass on the Platform Automation side quest: - Reset terraform/pipeline revision to master so the §2.4 pin-a-tag exercise starts from the right state - Sync §1.3 walkthrough with compute-env/main.tf (head VM size, worker ignore_changes, random_string, a note on the azcopy/Fusion start task) - Replace the $USER/$USERNAME interpolation mess with a single, dot-free WORKSHOP_USER handle set once and reused across the UI, tw, seqerakit and Terraform; tighten the Terraform username validation to reject dots - Register the page in mkdocs nav; refresh the §0 directory tree - Add seqerakit/launch-rnaseq-multiple.yml; drop per-directory READMEs - gitignore agent/terraform local state (.omc, .claude/.local, lock files) Generated by Claude Code

- !!! Tip -> !!! tip (lowercase type) - !!! Note Using a params.yml -> !!! note "Using a params file" (the unquoted title was parsed as CSS classes and dropped) Generated by Claude Code

adamrtalbot added 4 commits June 16, 2026 17:31

adamrtalbot added 4 commits June 17, 2026 11:47

fix(devcontainer): install tw via JAR on arm64

f9a5ef7

tower-cli publishes no tw-linux-arm64 asset, so the multi-arch image build 404'd on the arm64 leg. Keep the native binary on x86_64 and fall back to the arch-independent tw-jar.jar (run via Java) on arm64. Generated by Claude Code

docs(platform_automation): fix two malformed admonitions

9e8dc32

- !!! Tip -> !!! tip (lowercase type) - !!! Note Using a params.yml -> !!! note "Using a params file" (the unquoted title was parsed as CSS classes and dropped) Generated by Claude Code

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Add Seqera Platform Automation side quest#968

Add Seqera Platform Automation side quest#968
adamrtalbot wants to merge 8 commits into
masterfrom
platform-automation-side-quest

adamrtalbot commented Jun 16, 2026

Uh oh!

netlify Bot commented Jun 16, 2026 •

edited

Loading

Uh oh!

github-actions Bot commented Jun 16, 2026 •

edited

Loading

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

1 participant

Conversation

adamrtalbot commented Jun 16, 2026

Summary

Notes

Verification

Uh oh!

netlify Bot commented Jun 16, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

✅ Deploy Preview for nextflow-training ready!

Uh oh!

github-actions Bot commented Jun 16, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

1 participant

netlify Bot commented Jun 16, 2026 •

edited

Loading

github-actions Bot commented Jun 16, 2026 •

edited

Loading