[Do not merge!] Pseudo PR for first release#31

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mashehu wants to merge 202 commits intoTEMPLATEfrom

Commits on Jun 3, 2024

started building modules local, started on subworkflows
CaroAMN
committed

Commits on Jul 2, 2024

testing docker container
CaroAMN
committed

Commits on Aug 5, 2024

add intensity module
CaroAMN
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Commits on Aug 9, 2024

module:intensity, input/output fix
CaroAMN
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Commits on Aug 14, 2024

testing
CaroAMN
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testing
CaroAMN
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Commits on Aug 20, 2024

Commits on Sep 23, 2024

Commits on Sep 27, 2024

Commits on Oct 2, 2024

added registration module
CaroAMN
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Commits on Nov 13, 2024

Commits on Dec 20, 2024

update
CaroAMN
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Commits on Jan 8, 2025

update workflow
CaroAMN
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Commits on Jan 23, 2025

removed redundant file parsing
CaroAMN
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Commits on Jan 28, 2025

added: sample_sheet for processing multiple samples + workflow logic + meta map
CaroAMN
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Commits on Jan 29, 2025

Commits on Jan 30, 2025

Commits on Feb 2, 2025

added resample module
CaroAMN
committed

Commits on Feb 13, 2025

bug fix registration module + added into the full lsmquant workflow. update channels / dataflow between modules
CaroAMN
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Commits on Feb 17, 2025

Commits on Feb 18, 2025

added stubs
CaroAMN
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Commits on Feb 20, 2025

Commits on Feb 21, 2025

Commits on Feb 27, 2025

update process resources for full data run
CaroAMN
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Commits on Mar 19, 2025

update
CaroAMN
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Commits on Mar 20, 2025

Commits on Mar 21, 2025

Commits on Mar 24, 2025

Commits on Apr 1, 2025

bug fix in mat2json output + new metromap
CaroAMN
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Commits on May 9, 2025

new module for segmentation + gpu lable for segmentation process
CaroAMN
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Commits on May 16, 2025

update params_template, update documentation
CaroAMN
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Commits on May 19, 2025

fix numorph3dunet output + gpu access
CaroAMN
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Commits on May 20, 2025

adding nf-test-gpu.yml
CaroAMN
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Commits on May 28, 2025

Commits on Jun 4, 2025

update: convert symlinks
CaroAMN
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Commits on Jun 5, 2025

Commits on Jun 13, 2025

update nf-test config
CaroAMN
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Commits on Jun 18, 2025

Commits on Jun 20, 2025

Commits on Jun 25, 2025

Commits on Jun 27, 2025

Commits on Jul 3, 2025

update
CaroAMN
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Commits on Jul 15, 2025

Commits on Jul 21, 2025

Commits on Aug 19, 2025

Commits on Aug 20, 2025

testing gpu access
CaroAMN
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Commits on Aug 22, 2025

Commits on Aug 26, 2025

Commits on Aug 28, 2025

update pipeline level test + snapshot
CaroAMN
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Commits on Aug 29, 2025

Commits on Aug 30, 2025

Commits on Sep 1, 2025

Commits on Sep 2, 2025

update modules + container images
CaroAMN
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Commits on Sep 3, 2025

update nftignore, subworkflow(test)
CaroAMN
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Commits on Sep 4, 2025

Commits on Sep 5, 2025

Commits on Sep 22, 2025

Commits on Sep 23, 2025

adjusted mat2json process
CaroAMN
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Commits on Oct 7, 2025

new container for preprocessing, adjusting symlinks for files, fixing ara registration subworkflow
CaroAMN
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Commits on Oct 9, 2025

Commits on Oct 17, 2025

Commits on Oct 23, 2025

Commits on Oct 28, 2025

Commits on Oct 29, 2025

Commits on Nov 4, 2025

Merge pull request #32 from CaroAMN/dev
CaroAMN
authored

Commits on Nov 6, 2025

Commits on Nov 10, 2025

Merge pull request #35 from nf-core/fix-file-permissions
CaroAMN
authored

Commits on Nov 12, 2025

adding citations, remove typos
CaroAMN
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Commits on Nov 14, 2025

Commits on Dec 19, 2025

Apply suggestions from code review

CaroAMN
and
famosab
authored

Commits on Dec 23, 2025

Commits on Dec 29, 2025

Merge pull request #38 from CaroAMN/dev
CaroAMN
authored

Commits on Jan 2, 2026

Commits on Jan 7, 2026

update resource usage, fix input for large datasets
CaroAMN
committed

Commits on Jan 8, 2026