Major update to Nextflow for Genomics

[vdauwera]

Updates to the Genomics course

• Use of workflow level outputs
• Use modules from the start, improved how modules are introduced/explained
• Added a separate method overview section like RNAseq course
• Streamlined some parts to be more straightforward
• Improved instructions throughout
• Added command results etc

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[github-actions]

Nextflow linting complete!

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✅ 169 files had no errors
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Type	Location	Message
Error	hello-nf-core/solutions/core-hello-part2/nextflow.config:154:17	Invalid include source: '/home/runner/work/training/training/hello-nf-core/solutions/core-hello-part2/conf/test_full.config'

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', 'Holà') - .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','Holà'] + greetings_array = ['Hello', 'Bonjour', 'Holà'] // 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 } @@ -35,7 +35,7 @@ profiles { process.resourceLimits = [ memory: 750.GB, cpus: 200, - time: 30.d + time: 30.d, ... (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}' > '${greeting}-output.txt' """ }
hello-nf-core/solutions/core-hello-part2/conf/base.config	View @@ -11,13 +11,13 @@ process { // TODO nf-core: Check the defaults for all processes - cpus = { 1 * task.attempt } - memory = { 6.GB * task.attempt } - time = { 4.h * task.attempt } + cpus = { 1 * task.attempt } + memory = { 6.GB * task.attempt } + time = { 4.h * task.attempt } errorStrategy = { task.exitStatus in ((130..145) + 104 + 175) ? 'retry' : 'finish' } - maxRetries = 1 - maxErrors = '-1' + maxRetries = 1 ... (truncated)
hello-nf-core/solutions/core-hello-part2/conf/modules.config	View @@ -15,7 +15,6 @@ process { publishDir = [ path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, ] - }
hello-nf-core/solutions/core-hello-part2/conf/test.config	View @@ -14,18 +14,18 @@ process { resourceLimits = [ cpus: 2, memory: '4.GB', - time: '1.h' + time: '1.h', ] } params { - config_profile_name = 'Test profile' + config_profile_name = 'Test profile' config_profile_description = 'Minimal test dataset to check pipeline function' // Input data ... (truncated)
hello-nf-core/solutions/core-hello-part2/main.nf	View @@ -13,9 +13,9 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { HELLO } from './workflows/hello' +include { HELLO } from './workflows/hello' include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_hello_pipeline' -include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_hello_pipeline' +include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_hello_pipeline' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NAMED WORKFLOWS FOR PIPELINE @@ -26,7 +26,6 @@ include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_hell // WORKFLOW: Run main analysis pipeline depending on type of input // ... (truncated)
hello-nf-core/solutions/core-hello-part2/modules/local/collectGreetings.nf	View @@ -10,8 +10,8 @@ process collectGreetings { val batch_name output: - path "COLLECTED-${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 @@ -15,6 +15,6 @@ process cowpy { script: """ - cat $input_file | cowpy -c "$character" > cowpy-${input_file} + cat ${input_file} | cowpy -c "${character}" > cowpy-${input_file} """ }
hello-nf-core/solutions/core-hello-part2/modules/local/sayHello.nf	View @@ -13,6 +13,6 @@ process sayHello { script: """ - echo '$greeting' > '$greeting-output.txt' + echo '${greeting}' > '${greeting}-output.txt' """ }
hello-nf-core/solutions/core-hello-part2/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	View @@ -1,9 +1,9 @@ manifest { - 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' + name = 'nextflow_workflow' + author = """nf-core""" + homePage = 'https://127.0.0.1' + description = """Dummy pipeline""" + nextflowVersion = '!>=23.04.0' + version = '9.9.9' ... (truncated)
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hello-nf-core/solutions/core-hello-start/subworkflows/nf-core/utils_nfcore_pipeline/main.nf	(truncated)
hello-nf-core/solutions/core-hello-start/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config	(truncated)
hello-nf-core/solutions/core-hello-start/subworkflows/nf-core/utils_nfschema_plugin/main.nf	(truncated)
hello-nf-core/solutions/core-hello-start/workflows/hello.nf	(truncated)
nextflow-run/solutions/3-main.nf	(truncated)
nextflow-run/solutions/modules/collectGreetings.nf	(truncated)
nextflow-run/solutions/modules/convertToUpper.nf	(truncated)
nextflow-run/solutions/modules/sayHello.nf	(truncated)
nextflow-run/solutions/nextflow.config	(truncated)
side-quests/solutions/debugging/buggy_workflow.nf	(truncated)
side-quests/solutions/essential_scripting_patterns/main.nf	(truncated)

[ewels]

I haven't read / tested this, but given the time pressure - I trust you! 😅