Bump Nextflow training environment to 26.04.4

[pinin4fjords]

Bumps the training environment to Nextflow 26.04.4 (from 25.10.4) and refreshes the materials to match.

This is not a find-and-replace. Nextflow 26.04 makes the v2 syntax parser the default, and console output, file listings, and some behaviours change versus 25.10. Every runnable tutorial was re-run end-to-end on 26.04.4 (in Docker, NXF_VER=26.04.4) and its documented output regenerated from genuine runs. No fabricated or hand-edited output.

What changed

• NXF_VER → 26.04.4 in both devcontainer configs.
• info/nxf_versions.md rewritten: the "v2 parser will become the default in 26.04" statements are now present-tense, and the loaded-version note is 26.04.4. The supported floor stays 25.10.2 (still valid with the v2 parser enabled).
• All console blocks, Outputs: summaries, error text, and file listings refreshed from real 26.04.4 runs across the modules below.

Verified on 26.04.4 (default v2 parser)

• hello_nextflow (Parts 1-6)
• nextflow_run + envsetup
• nf4_science — genomics + rnaseq (VCFs byte-matched) and imaging/molkart (full 22-task run on native x86)
• side_quests — all 9 (debugging, dev_environment, essential_scripting_patterns, metadata, nf_test, plugin_development, splitting_and_grouping, workflows_of_workflows, working_with_files), each verified by a dedicated run
• Consistency pass: heading numbering, prettier, hl_lines, internal hash consistency

Confirmed across every module: 26.04 required no script changes — the v2-syntax scripts already parse and run cleanly. All real changes are console-output formatting: the version banner, the Launching line dropping DSL2, the process status line ([hash] NAME | N of M ✔), and the new end-of-run Outputs: summary block.

Incidental fixes (found along the way)

• hello_nextflow/04: stale greeting param corrected to input (mismatched the solution; would null params.input).
• hello_nextflow/05 + nextflow_run/02: cowpy demos used the positional form (cowpy "Hello Containers"), which doesn't put the text in the speech bubble (cowpy reads stdin). Switched to the stdin form so the documented output matches, consistent with how the pipeline module invokes cowpy.
• nf4_science/rnaseq/03: MultiQC data-dir listing refreshed to current tool output.
• nf4_science/imaging: was lagging at 25.04.3; brought up to 26.04 and made v2-safe by switching molkart's documented integer params from CLI flags (which arrive as strings under the v2 parser and fail validation) to a typed params.yaml. Also fixed a fabricated resume block and a wrong task count.

Deliberately scoped out (one follow-up)

• hello_nf-core stays on the v1 parser in this PR (orientation instructs export NXF_SYNTAX_PARSER=v1). The course is verified working end-to-end on 26.04.4 under v1 (Part 1's nextflow pull exploration steps were updated for 26.04's new on-disk layout, and the full nf-core/demo run completes). Running it under the v2 default needs a content change (the nf-core --validate_params false CLI pattern is a no-op under v2 — Using strict syntax causes template to raise an error when setting boolean options on CLI nf-core/tools#4100, still open) and a migration to the nf-core tools 4.0 template. That modernization is a stacked follow-up PR (hello-nf-core-tools-4.0, solutions already migrated and verified).

Translations

docs/<lang>/ are out of scope here; they are regenerated by the separate translation pipeline.

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Nextflow linting complete!

⚠️ 35 files had 70 warnings
✅ 189 files had no errors
🔧 136 files would be changed by auto-formatting

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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)
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