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‎CHANGELOG.md‎

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# task_batch_integration x.y.z
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# task_batch_integration 2.0.0
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## BREAKING CHANGES
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A major update to the OpenProblems framework, switching from a Python-based framework to a Viash + Nextflow-based framework. This update features the same concepts as the previous version, but with a new implementation that is more flexible, scalable, and maintainable.
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<!-- * Restructured `src` directory (PR #3). -->
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## Migration
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## NEW FUNCTIONALITY
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* Added expected input/output interfaces in `src/api` and document them in `README.md`.
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* Added `control_methods/true_labels` component (PR #5).
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* Store common resources used across tasks in a git submodule `common`.
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* Added `methods/logistic_regression` component (PR #5).
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* Methods, metrics, workflows and other components are implemented as Viash components with a per-component Docker image.
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* Added `metrics/accuracy` component (PR #5).
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## New functionality
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## MAJOR CHANGES
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* Switched to larger datasets derived from CELLxGENE.
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* Updated `api` files (PR #5).
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* Added SCimilarity (PR #3).
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* Updated configs, components and CI to the latest Viash version (PR #8).
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* Added Geneformer (PR #6).
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## MINOR CHANGES
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* Added UCE method (PR #7).
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* Updated `README.md` (PR #5).
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* Added scGPT zero shot (PR #8, #16).
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## BUGFIXES
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* Added scPRINT (PR #13).
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* Added scGPT fine-tuned (PR #17).
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## Major changes
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* Prefilter batches in HVG overlap metric (PR #9).
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* Precompute clustering for some metrics (PR #18).
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## Minor changes
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* Add arguments for filtering methods in benchmarking workflow (PR #4).
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* Update compute environment (PR #5).
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* Adjust resources (PR #10).
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* Update dependency components (PR #10).
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* Update API formats (PR #21, #28, #31).
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* Add support for zebrafish and C. elegans (PR #22).
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* Bump scIB to v1.1.7 (PR #30).
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* Update common submodule (PR #29).
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## Bug fixes
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* Multiple fixes prior to release (PR #24, #25, #26, #27, #32, #34, #36, #37, #39, #41, #42, #43, #44).
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## Documentation
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* Update documentation (PR #45).
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# task_batch_integration 1.0.0
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This version can be found [here](https://github.com/openproblems-bio/openproblems/tree/v1.0.0/openproblems/tasks/_batch_integration).

‎_viash.yaml‎

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github: danielStrobl
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orcid: 0000-0002-5516-7057
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- name: Robrecht Cannoodt
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roles: [contributor]
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roles: [author]
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info:
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github: rcannood
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orcid: "0000-0003-3641-729X"
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- name: Luke Zappia
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roles: [author]
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info:
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github: lazappi
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orcid: 0000-0001-7744-8565
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- name: "Scott Gigante"
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roles: [contributor]
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info:
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info:
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github: KaiWaldrant
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orcid: "0009-0003-8555-1361"
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- name: Nartin Kim
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- name: Martin Kim
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roles: [contributor]
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info:
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github: martinkim0
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orcid: "0009-0003-8555-1361"
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- name: Sai Nirmayi Yasa
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roles: [contributor]
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info:
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github: sainirmayi
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orcid: 0009-0003-6319-9803
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config_mods: |
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.runners[.type == "nextflow"].config.labels := { lowmem : "memory = 20.Gb", midmem : "memory = 50.Gb", highmem : "memory = 100.Gb", lowcpu : "cpus = 5", midcpu : "cpus = 15", highcpu : "cpus = 30", lowtime : "time = 1.h", midtime : "time = 4.h", hightime : "time = 8.h", veryhightime : "time = 24.h" }
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repositories:

‎target/executable/control_methods/embed_cell_types/.config.vsh.yaml‎

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output: "target/executable/control_methods/embed_cell_types"
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executable: "target/executable/control_methods/embed_cell_types/embed_cell_types"
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viash_version: "0.9.0"
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git_commit: "df3f053963c3a9a98e95c31b8e91236413be5839"
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git_commit: "3794a9236827cded1e89c2d9b5a858b977ce7609"
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git_remote: "https://github.com/openproblems-bio/task_batch_integration"
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package_config:
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name: "task_batch_integration"
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orcid: "0000-0002-5516-7057"
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- name: "Robrecht Cannoodt"
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roles:
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- "contributor"
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- "author"
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info:
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github: "rcannood"
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orcid: "0000-0003-3641-729X"
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- name: "Luke Zappia"
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roles:
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- "author"
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info:
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github: "lazappi"
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orcid: "0000-0001-7744-8565"
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- name: "Scott Gigante"
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roles:
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- "contributor"
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info:
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github: "KaiWaldrant"
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orcid: "0009-0003-8555-1361"
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- name: "Nartin Kim"
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- name: "Martin Kim"
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roles:
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- "contributor"
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info:
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github: "martinkim0"
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orcid: "0009-0003-8555-1361"
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- name: "Sai Nirmayi Yasa"
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roles:
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- "contributor"
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info:
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github: "sainirmayi"
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orcid: "0009-0003-6319-9803"
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keywords:
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- "batch integration"
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- "scRNA-seq"

‎target/executable/control_methods/embed_cell_types/embed_cell_types‎

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FROM openproblems/base_python:1.0.0
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ENTRYPOINT []
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LABEL org.opencontainers.image.description="Companion container for running component control_methods embed_cell_types"
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LABEL org.opencontainers.image.created="2025-02-11T12:19:19Z"
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LABEL org.opencontainers.image.created="2025-02-11T13:19:16Z"
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LABEL org.opencontainers.image.source="https://github.com/openproblems-bio/task_batch_integration"
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LABEL org.opencontainers.image.revision="df3f053963c3a9a98e95c31b8e91236413be5839"
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LABEL org.opencontainers.image.revision="3794a9236827cded1e89c2d9b5a858b977ce7609"
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LABEL org.opencontainers.image.version="2.0.0"
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VIASHDOCKER

‎target/executable/control_methods/embed_cell_types_jittered/.config.vsh.yaml‎

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output: "target/executable/control_methods/embed_cell_types_jittered"
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executable: "target/executable/control_methods/embed_cell_types_jittered/embed_cell_types_jittered"
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viash_version: "0.9.0"
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git_commit: "df3f053963c3a9a98e95c31b8e91236413be5839"
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git_commit: "3794a9236827cded1e89c2d9b5a858b977ce7609"
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git_remote: "https://github.com/openproblems-bio/task_batch_integration"
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package_config:
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name: "task_batch_integration"
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orcid: "0000-0002-5516-7057"
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- name: "Robrecht Cannoodt"
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roles:
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- "contributor"
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- "author"
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info:
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github: "rcannood"
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orcid: "0000-0003-3641-729X"
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- name: "Luke Zappia"
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roles:
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- "author"
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info:
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github: "lazappi"
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orcid: "0000-0001-7744-8565"
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- name: "Scott Gigante"
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- "contributor"
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info:
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github: "KaiWaldrant"
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orcid: "0009-0003-8555-1361"
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- name: "Nartin Kim"
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- name: "Martin Kim"
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roles:
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- "contributor"
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info:
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github: "martinkim0"
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orcid: "0009-0003-8555-1361"
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- name: "Sai Nirmayi Yasa"
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roles:
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- "contributor"
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info:
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github: "sainirmayi"
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orcid: "0009-0003-6319-9803"
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keywords:
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- "batch integration"
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- "scRNA-seq"

‎target/executable/control_methods/embed_cell_types_jittered/embed_cell_types_jittered‎

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FROM openproblems/base_python:1.0.0
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ENTRYPOINT []
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LABEL org.opencontainers.image.description="Companion container for running component control_methods embed_cell_types_jittered"
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LABEL org.opencontainers.image.created="2025-02-11T12:19:18Z"
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LABEL org.opencontainers.image.created="2025-02-11T13:19:16Z"
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LABEL org.opencontainers.image.source="https://github.com/openproblems-bio/task_batch_integration"
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LABEL org.opencontainers.image.revision="df3f053963c3a9a98e95c31b8e91236413be5839"
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LABEL org.opencontainers.image.revision="3794a9236827cded1e89c2d9b5a858b977ce7609"
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LABEL org.opencontainers.image.version="2.0.0"
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VIASHDOCKER

‎target/executable/control_methods/no_integration/.config.vsh.yaml‎

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output: "target/executable/control_methods/no_integration"
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executable: "target/executable/control_methods/no_integration/no_integration"
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viash_version: "0.9.0"
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git_commit: "df3f053963c3a9a98e95c31b8e91236413be5839"
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git_commit: "3794a9236827cded1e89c2d9b5a858b977ce7609"
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git_remote: "https://github.com/openproblems-bio/task_batch_integration"
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package_config:
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name: "task_batch_integration"
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- name: "Robrecht Cannoodt"
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roles:
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- "contributor"
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- "author"
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info:
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github: "rcannood"
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orcid: "0000-0003-3641-729X"
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- name: "Luke Zappia"
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roles:
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- "author"
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info:
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github: "lazappi"
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orcid: "0000-0001-7744-8565"
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- "contributor"
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info:
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github: "KaiWaldrant"
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orcid: "0009-0003-8555-1361"
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- name: "Nartin Kim"
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- name: "Martin Kim"
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roles:
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- "contributor"
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info:
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github: "martinkim0"
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orcid: "0009-0003-8555-1361"
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- name: "Sai Nirmayi Yasa"
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roles:
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- "contributor"
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info:
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github: "sainirmayi"
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orcid: "0009-0003-6319-9803"
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keywords:
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- "batch integration"
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- "scRNA-seq"

‎target/executable/control_methods/no_integration/no_integration‎

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FROM openproblems/base_python:1.0.0
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ENTRYPOINT []
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LABEL org.opencontainers.image.description="Companion container for running component control_methods no_integration"
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LABEL org.opencontainers.image.created="2025-02-11T12:19:18Z"
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LABEL org.opencontainers.image.created="2025-02-11T13:19:15Z"
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LABEL org.opencontainers.image.source="https://github.com/openproblems-bio/task_batch_integration"
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LABEL org.opencontainers.image.revision="df3f053963c3a9a98e95c31b8e91236413be5839"
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LABEL org.opencontainers.image.revision="3794a9236827cded1e89c2d9b5a858b977ce7609"
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LABEL org.opencontainers.image.version="2.0.0"
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VIASHDOCKER

‎target/executable/control_methods/no_integration_batch/.config.vsh.yaml‎

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output: "target/executable/control_methods/no_integration_batch"
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viash_version: "0.9.0"
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git_commit: "df3f053963c3a9a98e95c31b8e91236413be5839"
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git_commit: "3794a9236827cded1e89c2d9b5a858b977ce7609"
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git_remote: "https://github.com/openproblems-bio/task_batch_integration"
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package_config:
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name: "task_batch_integration"
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- name: "Robrecht Cannoodt"
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roles:
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- "contributor"
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- "author"
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info:
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github: "rcannood"
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orcid: "0000-0003-3641-729X"
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- name: "Luke Zappia"
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roles:
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- "author"
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info:
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github: "lazappi"
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orcid: "0000-0001-7744-8565"
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- name: "Scott Gigante"
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- "contributor"
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info:
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github: "KaiWaldrant"
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orcid: "0009-0003-8555-1361"
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- name: "Nartin Kim"
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- name: "Martin Kim"
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roles:
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- "contributor"
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info:
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github: "martinkim0"
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orcid: "0009-0003-8555-1361"
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- name: "Sai Nirmayi Yasa"
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roles:
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- "contributor"
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info:
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github: "sainirmayi"
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orcid: "0009-0003-6319-9803"
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keywords:
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- "batch integration"
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- "scRNA-seq"

‎target/executable/control_methods/no_integration_batch/no_integration_batch‎

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FROM openproblems/base_python:1.0.0
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ENTRYPOINT []
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LABEL org.opencontainers.image.description="Companion container for running component control_methods no_integration_batch"
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LABEL org.opencontainers.image.created="2025-02-11T12:19:19Z"
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LABEL org.opencontainers.image.created="2025-02-11T13:19:16Z"
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LABEL org.opencontainers.image.source="https://github.com/openproblems-bio/task_batch_integration"
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LABEL org.opencontainers.image.revision="df3f053963c3a9a98e95c31b8e91236413be5839"
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LABEL org.opencontainers.image.revision="3794a9236827cded1e89c2d9b5a858b977ce7609"
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LABEL org.opencontainers.image.version="2.0.0"
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VIASHDOCKER

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