Tags: NahkuriR/training
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Update advanced training to current syntax (nextflow-io#641) * (feat): Update advanced training to new syntax Updates to the advanced training to use the current syntax making it more consistent with the other guides. Changes: - Replace all pipe operators with method chaining - Where required, assigns to intermediate channel and uses in a process - Moves all logic into workflows * chore: update starting code * fix: Name all iterators in closures * chore: remove extra files * fix: add all named closures within workflow scope * fix: Use def for every new variable * fix: do not use same variable name twice * fix: remove variables that are not used * fix: multiMap syntax * fix: add block to every process * feat: adds checkIfExists to block users accidentally missing step * fix: Add period to beginning of map to make copy+paste easier * fix: add grouping starter back * style: code style in grouping.md * fix: MapReads assigning output * fix: review fixups * fix: Groovy training * fix: structure training inconsistencies * Apply suggestion from @FriederikeHanssen Co-authored-by: Friederike Hanssen <friederike.hanssen@seqera.io> * Update docs/advanced/operators.md Co-authored-by: Friederike Hanssen <friederike.hanssen@seqera.io> * Update docs/advanced/operators.md Co-authored-by: Friederike Hanssen <friederike.hanssen@seqera.io> * docs: update advanced grouping training to new syntax - Update grouping.md documentation with modern Nextflow syntax - Modify main.nf workflow to use current DSL2 conventions - Remove deprecated working_with_files/main.nf file - Improve code examples and explanations for better learning experience * feat: add structure training examples with Groovy classes - Add Dog.groovy and Metadata.groovy classes for structure training - Update main.nf workflow to demonstrate class usage and imports - Modify cars.R script for better R integration example - Update structure.md documentation with new examples - Demonstrate proper project structure with lib/ directory * style: Highlight code in operator tour * style: Highlight code in metadata * style: Line numbers and highlighting in operators * style: Line numbers and highlighting in metadata * style: Line numbers and highlighting in grouping * fixup * fixup * style: Line numbers and highlighting in groovy * style: Line numbers and highlighting in structure --------- Co-authored-by: Friederike Hanssen <friederike.hanssen@seqera.io>
First pass of the Nextflow Run course (nextflow-io#626) Abridged version of Hello Nextflow focused on running rather than developing. - Run basic operations (Hello World level) - Run pipelines (channels for multiple inputs, multi-step example, modules, containers) - Configuration
Splitting and grouping side quest (nextflow-io#595) * First draft of splitting and grouping side quest First draft of a splitting and grouping side quest. This includes separating samples using filter, then grouping and spreading by intervals. Early version but introduces key operator concepts to participants. * Spread over intervals prior to grouping This commit reverses the order to spread over intervals prior to grouping. This achieves two things: 1. It explains everything once and only once to make the tutorial simpler 2. It provides a real world reason for using groupTuple This makes the flow of the tutorial easier to understand, at the cost of very verbose outputs. * add splitting and grouping to nav bar * Add before/after to first code change * Add ch_* prefix to all channels for clarity over objects * Remove "pipeline" from opening statement to focus on channels * Add "you will" statement to the beginning of the tutorial * Fix typo and phrasing about combining * Refine explanation of intervals and the combining method * add another before/after snippet * Use single BAM as input file * Remove dump from tutorial to simplify and focus splitting-grouping and not debugging * Update samplesheet * fixup: Remove TODO * Finish with a section on flattening the data to close out grouping * revert main.nf * Sort out notes * Re-order side quests slightly for more logical order, from least to most complex * remove intervals file * Add earlier map to simplify data as core concept instead of challenge * Tidy code up a bit * Fix side quest order * Reduce examples and left shift for clarity * Fix typo in path to splitting-and-grouping * Fix samplesheet items to be more consistent * More consistent phrasing of first steps * Apply suggestions from code review Co-authored-by: Friederike Hanssen <friederike.hanssen@seqera.io> * Add reference to join documentation * Fix headers and indentation * Rename splitting and grouping file to be consistent with other filenames * Refine summary messages * Use bullet points instead of numbers for key concepts of splitting-and-grouping * splitting and grouping use before/after correctly * Splitting and grouping highlight lines * fixup * Fix formatting issue --------- Co-authored-by: Friederike Hanssen <friederike.hanssen@seqera.io>
Italian translation of 'Hello Nextflow' (nextflow-io#590) - Translates Hello Nextflow into Italian - Updates code blocks to the new structure - Small fixes --------- Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io> Co-authored-by: Giada Bellofatto <g.bellofatto2@studenti.unisa.it> Co-authored-by: MaraStanco <M.STANCO15@studenti.unisa.it> Co-authored-by: elisa270401 <e.dati@studenti.unisa.it> Co-authored-by: SaraPappacena <pappacenasara@gmail.com> Co-authored-by: Antonio8910 <a.barra25@studenti.unisa.it> Co-authored-by: annapaolagr <a.grimaldi122@studenti.unisa.it> Co-authored-by: Margherita <86382379+daisymut@users.noreply.github.com> Co-authored-by: ianniellomaria <m.ianniello23@studenti.unisa.it>
Docs: Deploy master as 'development' version (nextflow-io#574) * Docs: Deploy master as 'development' version * Rename to 0dev to sort to the bottom * Standardise GitHub action names and filenames * Update path filter
Minor updates to navigation and Side Quests index, orientation (nextf… …low-io#563) * Updated index and orientation pages for Side Quests * Updated navigation menu to follow home page listing * Fix capitalization in genomics docs + renumber the placeholder for the config section to avoid confusion * Rename Launch to Start on Home page to disambiguate starting a training vs launching the environment
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