Bump nf-co2footprint to 1.3.0, remove config-warning workaround by pinin4fjords · Pull Request #950 · nextflow-io/training

pinin4fjords · 2026-05-08T11:45:01Z

Summary

Bump nf-co2footprint plugin pin in the plugin-basics side quest from 1.2.0 to 1.3.0.
Remove the !!! note admonition that told learners to ignore the cosmetic WARN: Unrecognized config option 'co2footprint.location' message.
Bump NXF_VER in .devcontainer/devcontainer.json from 25.10.4 to 26.04.0 (required by plugin 1.3.0, see below).

The upstream fix landed in nf-co2footprint 1.3.0:

Eliminated Unrecognized config option warnings under Nextflow's v2 syntax parser by registering CO2FootprintConfig as an extension point and aligning the nested file-config scopes with the v2 ConfigScope discovery rules

Draft - Nextflow version implication

nf-co2footprint@1.3.0 declares a minimum Nextflow version of 26.04.0, so the devcontainer pin had to move up too. Confirmed locally:

Failed requirement - Plugin nf-co2footprint@1.3.0 requires Nextflow version >=26.04.0 (current 25.10.2)

After bumping NXF_VER=26.04.0, the plugin loads cleanly and the cosmetic warning is gone.

This is left as draft because bumping NXF_VER will affect every other tutorial under docs/en/. There are roughly 30+ console-output snippets across hello_nextflow/, nf4_science/, etc. that show N E X T F L O W ~ version 25.10.x, plus prose like "This training is designed for Nextflow 25.10.x or later" in index.md and orientation pages. Those will look stale to anyone running the training off this branch.

Open questions for reviewers:

Do we want to do a coordinated NXF_VER bump (touching all 25.10.x references) before merging this?
Or split: ship a smaller PR that only updates the side quest, keeping the plugin pin at 1.2.0 and rephrasing the workaround note to point at 1.3.0 + Nextflow 26?
Or wait for an org-wide "bump to 26" PR and rebase this on top?

Test plan

Verified locally with Docker (ghcr.io/nextflow-io/training:latest, NXF_VER=26.04.0) that nextflow run hello.nf against the section 3.4 config emits no Unrecognized config option warning.
Verified the GB-specific carbon intensity (163.92 gCO₂eq/kWh) is still applied as documented.
CI / docs build
Reviewer confirms the broader version-bump strategy

🤖 Generated with Claude Code

The 1.3.0 release registers `CO2FootprintConfig` as a `ConfigScope` extension point, so the cosmetic `WARN: Unrecognized config option 'co2footprint.location'` no longer appears. Drop the note that told learners to ignore it. 1.3.0 requires Nextflow >=26.04.0, so bump NXF_VER in the devcontainer. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

netlify · 2026-05-08T11:45:07Z

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github-actions · 2026-05-08T11:45:49Z

Nextflow linting complete!

⚠️ 24 files had 53 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 53 issues

Type	Location	Message
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_nfcore_pipeline/main.nf:16:5	Variable was declared but not used
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_nfcore_pipeline/main.nf:16:5	Variable was declared but not used
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_nfcore_pipeline/main.nf:16:5	Variable was declared but not used
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_nfcore_pipeline/main.nf:16:5	Variable was declared but not used
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_nfcore_pipeline/main.nf:16:5	Variable was declared but not used
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	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

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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)
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Bump nf-co2footprint to 1.3.0, remove config-warning workaround#950

Bump nf-co2footprint to 1.3.0, remove config-warning workaround#950
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pinin4fjords commented May 8, 2026

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