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Add Workflow Run RO-crate format#39

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bentsherman merged 58 commits intonextflow-io:masternextflow-io/nf-prov:masterfrom famosab:dev-wrrocfamosab/nf-prov:dev-wrrocCopy head branch name to clipboardFeb 6, 2025

+1,105-22

Commits

Commits on Nov 18, 2024

• status from PR nextflow-io#33

  famosab

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• add encodingFormat for nextflow.config

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• add encodingFormat for main.nf

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Commits on Dec 3, 2024

• Merge pull request #10 from famosab/encode

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• feat: add wrroc to valid formats

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• Merge pull request #13 from famosab/obs

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Commits on Dec 6, 2024

• fix: make getIntermediateOutputFiles work again (#18)

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Commits on Dec 8, 2024

• Check in input and output if file or directory

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Commits on Dec 9, 2024

• feat: add README to crate (#14)

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• Set correct MIME types

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Commits on Dec 13, 2024

• Add contactPoint for agent and organization (#21)

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• Fix #4 (#22)

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Commits on Dec 17, 2024

• Merge branch 'dev-wrroc' into iss7-directoryType

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• Merge pull request #20 from famosab/iss7-directoryType

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Commits on Dec 18, 2024

• start with metaYaml imports (#12)

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• add information to README

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Commits on Jan 10, 2025

• cleanup

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Commits on Jan 14, 2025

• Set root crate dir to parent of wrroc path

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• cleanup

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• Add helper functions

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• Don't copy intermediate files into crate, normalize inputs against project dir

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• Fix resolved config

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• Add CreateAction's for publishing outputs

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• minor fix

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• Improve ids for modules, processes, tools, replace main script with repository URL + commit hash

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• cleanup

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• cleanup config parsing

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• cleanup

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• Improve canonical ids

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• Use parameter schema to populate formal parameters, copy input files

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Commits on Jan 16, 2025

• Exclude null property values

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• Include permalink to main script

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• Add cases for lists and maps for formal parameters

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• Don't download remote input files into crate

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• Include main script to satisfy WRROC requirement

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• Replace "Directory" -> "Dataset"

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Commits on Jan 17, 2025

• Exclude (and warn about) published files outside of crate directory

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• Fix tool description, cleanup

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• Add param input files to dataset parts

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• Improve canonical ids for tasks and task outputs

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• Fix validation issues

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• Separate staged input files from workflow inputs

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• Update docs, fix issues with wrroc config options

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• Fix null reference error

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• Don't copy directories specified by params into crate

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• minor edits

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• Improve entity ids

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• Make intermediate outputs into contextual entities (CreativeWork)

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Commits on Jan 22, 2025

• Exclude license entity if it is not specified

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• Fix null reference error when agent is not specified

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Commits on Jan 23, 2025

• Add warning if pipeline repo URL can't be determined

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Commits on Jan 27, 2025

• Use heuristic to identify original definition of task processor

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• Encode missing input files as absolute URIs

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Commits on Feb 3, 2025

• Separate ro-crate license from pipeline license

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• Normalize durations and memory units as raw numbers

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Commits on Feb 4, 2025

• Update warning about unknown parameter type

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• Handle task inputs from work/tmp/

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• Exclude parameters set to null

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