Nextflow translator, Nextflow/Streamflow/RO-Crate log parser rewrites/re-orgs - #162

Merged

henricasanova merged 38 commits into

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nextflow_translator_ro_crate_log_parsers_rewrite

Jun 30, 2026

Commits on Jun 25, 2026

Translator / Logger updates (RO-Crate, Nextflow)
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a7153c6
Re-establishing all tests as before
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8cad889
Removing unneeded import
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823973a
Temporary Fix revert in the RO-Crate log parser
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41593a1
Updated matplotlib colormap call
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9d99ef8
colormap (real) fix
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87b5ded
Re-establishing all tests
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800ea04

Commits on Jun 26, 2026

RO-Crate parsing fix for a Nextflow workflow
henricasanova
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2cb8795
Added a way to get task times from Nextflow executions (because RO-Crate
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386e4d7
Improved RO-Crate parsing for Nextflow
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b6fc1f8
Re-enabled all tests
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939beca
Made the RO-Crate log parser handle file sizes correctly for
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bd26c58
Added task id sanitization to the RO-Crate log parser
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e2d2b1d
Re-establishing all tests
henricasanova
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2fcfb71

Commits on Jun 27, 2026

For Nextflow/RO-Crate parsing, makde is so that if multiple trace
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026af2d

Commits on Jun 28, 2026

Commits on Jun 29, 2026

tweaks
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8cf5d50
tmp commit
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3bfe63f
Added trace creation to the (translated) nextflow execution
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d98d69c
Merge branch 'nextflow_log_parser' into nextflow_log_parser_refactored
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48043fd
Streamflow/Nextflow/RO-Crate code refactoring
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2d8285f
More code re-factoring
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97d6e58
debug
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ba44621
More code re-factoring
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c3d89fc
Merge branch 'nexflow_translator' into tmp_branch
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2a2663c
Added RO-Crate detectable workflow input files for nextflow translator
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59c7580
RE-established all tests
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081f528

Commits on Jun 30, 2026

Made nextflow translator a bit more robust
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09f752e
More robustness
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c0be411
More robustness?
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4b04be7
Commented-out all "single file" code in the nextflow translator
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d706627
Re-established all tests
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10a3c87
Made nextflow translator code work on Python 3.11
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7a938e9
Merge branch 'main' into nextflow_translator_ro_crate_log_parsers_rewrite
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5ed2792
Re-establishing all tests
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07a46d8