First release! by @heylf @khersameesh24 @an-altosian

What’s Changed

• installed xeniumranger modules, removed fastqc by @khersameesh24 in https://github.com/nf-core/spatialaxe/pull/30
• added pipeline metromap, updated README page by @khersameesh24 in https://github.com/nf-core/spatialaxe/pull/34
• suggested changes to metro map by @khersameesh24 in https://github.com/nf-core/spatialaxe/pull/39
• 32 update pipeline metro map on the readme page by @khersameesh24 in https://github.com/nf-core/spatialaxe/pull/40
• 32 update pipeline metro map on the readme page by @khersameesh24 in https://github.com/nf-core/spatialaxe/pull/36
• ïnstalled module xeniumranger resegment by @khersameesh24 in https://github.com/nf-core/spatialaxe/pull/46
• New module cellpose by @khersameesh24 in https://github.com/nf-core/spatialaxe/pull/45
• Add nf core module cellpose by @heylf in https://github.com/nf-core/spatialaxe/pull/48
• Add local module proseg by @khersameesh24 in https://github.com/nf-core/spatialaxe/pull/44
• Local module proseg by @khersameesh24 in https://github.com/nf-core/spatialaxe/pull/49
• outdated dev by @heylf in https://github.com/nf-core/spatialaxe/pull/56
• Important! Template update for nf-core/tools v3.2.0 by @nf-core-bot in https://github.com/nf-core/spatialaxe/pull/50
• add resolift module with test by @kubranarci in https://github.com/nf-core/spatialaxe/pull/62
• Big big update for spatialxe dev by @heylf in https://github.com/nf-core/spatialaxe/pull/67
• Add subworkflow segger by @khersameesh24 in https://github.com/nf-core/spatialaxe/pull/68
• Add subworkflow proseg by @khersameesh24 in https://github.com/nf-core/spatialaxe/pull/70
• Add subworkflow ficture - to merged after merging the proseg subworkflow PR by @khersameesh24 in https://github.com/nf-core/spatialaxe/pull/72
• added baysor subworkflow, minor changes to config, resolift by @khersameesh24 in https://github.com/nf-core/spatialaxe/pull/76
• Add subworkflow xeniumranger by @khersameesh24 in https://github.com/nf-core/spatialaxe/pull/79
• Add subworkflow cellpose by @khersameesh24 in https://github.com/nf-core/spatialaxe/pull/80
• Add subworkflow baysor/proseg - transcript assignment inputs by @khersameesh24 in https://github.com/nf-core/spatialaxe/pull/81
• added subworklfow for cellpose->bayor->imp-seg, nextflow schema by @khersameesh24 in https://github.com/nf-core/spatialaxe/pull/83
• Major Linting fix update, moving to nf-core standards, schema fixes, module patches for cellpose, xr modules by @khersameesh24 in https://github.com/nf-core/spatialaxe/pull/85
• Important! Template update for nf-core/tools v3.2.1 by @nf-core-bot in https://github.com/nf-core/spatialaxe/pull/84
• Added pipeline run modes (—mode) - image & coordinate, fixed schema, config, updated readme by @khersameesh24 in https://github.com/nf-core/spatialaxe/pull/86
• Changed transcript handling from csv to parquet by @khersameesh24 in https://github.com/nf-core/spatialaxe/pull/88
• Update metromap by @heylf in https://github.com/nf-core/spatialaxe/pull/90
• Couple of fixes by @heylf in https://github.com/nf-core/spatialaxe/pull/92
• choice of segmentation, changes to baysor, updated metromap by @khersameesh24 in https://github.com/nf-core/spatialaxe/pull/95
• Changes to spatialdata handling based on coordinate space by @khersameesh24 in https://github.com/nf-core/spatialaxe/pull/98
• Important! Template update for nf-core/tools v3.3.2 by @nf-core-bot in https://github.com/nf-core/spatialaxe/pull/93
• Massive linting fixes and other minor changes by @khersameesh24 in https://github.com/nf-core/spatialaxe/pull/99
• Added new module and subworkflow for opt, Ci fix changes by @khersameesh24 in https://github.com/nf-core/spatialaxe/pull/101
• Multisample support for spatialxe runs by @khersameesh24 in https://github.com/nf-core/spatialaxe/pull/102
• Testing changes and code formatting by @khersameesh24 in https://github.com/nf-core/spatialaxe/pull/103
• Important! Template update for nf-core/tools v3.4.1 by @nf-core-bot in https://github.com/nf-core/spatialaxe/pull/105
• Merge baysor preview html in multiqc report by @khersameesh24 in https://github.com/nf-core/spatialaxe/pull/108
• Placeholder module until multiqc supports baysor by @khersameesh24 in https://github.com/nf-core/spatialaxe/pull/111
• Fix multiqc_title param missing —title flag by @mcmero in https://github.com/nf-core/spatialaxe/pull/114
• feat: xenium patch tiling, cellpose/stardist updates, and processing improvements by @an-altosian in https://github.com/nf-core/spatialaxe/pull/123
• feat: xenium patch tiling/stitching, cellpose downscaling, module updates, and bug fixes by @an-altosian in https://github.com/nf-core/spatialaxe/pull/133
• fix: correct release-announcements.yml to match nf-core template by @an-altosian in https://github.com/nf-core/spatialaxe/pull/134
• Changes to documentiation and subway map by @heylf in https://github.com/nf-core/spatialaxe/pull/135
• preparing for release, bumping version to 1.0.0 by @heylf in https://github.com/nf-core/spatialaxe/pull/136
• linting test fixed by @heylf in https://github.com/nf-core/spatialaxe/pull/137
• label was missing in metromap by @heylf in https://github.com/nf-core/spatialaxe/pull/138
• disabled conda profile for nf-test by @khersameesh24 in https://github.com/nf-core/spatialaxe/pull/140
• mainly changes to documentation by @heylf in https://github.com/nf-core/spatialaxe/pull/141
• feat: add meta.yml for local modules + extract RECONSTRUCT_PATCHES (closes #142) by @an-altosian in https://github.com/nf-core/spatialaxe/pull/143
• fix: dual-form containers + pandas 3 compatibility for utility modules by @an-altosian in https://github.com/nf-core/spatialaxe/pull/144
• addressing review comments for release by @heylf in https://github.com/nf-core/spatialaxe/pull/147
• Address PR #139 review: segger refactor + 5 targeted fixes by @an-altosian in https://github.com/nf-core/spatialaxe/pull/148
• refactor(workflows/spatialxe): extract params.* to take: inputs by @an-altosian in https://github.com/nf-core/spatialaxe/pull/150
• refactor: extract inline Python from 5 modules to module binaries (P1/P2 sweep) by @an-altosian in https://github.com/nf-core/spatialaxe/pull/151
• refactor(subworkflows): extract params.* to take: inputs across 13 subworkflows by @an-altosian in https://github.com/nf-core/spatialaxe/pull/152
• bugfixes from previous PRs by @heylf in https://github.com/nf-core/spatialaxe/pull/153
• refactor(modules): convert all 19 module-level bin scripts to Nextflow templates by @an-altosian in https://github.com/nf-core/spatialaxe/pull/154
• removed redundant files under modules/<name>/resource/usr/bin/<script> by @khersameesh24 in https://github.com/nf-core/spatialaxe/pull/155
• fix for reviewer suggestions by @khersameesh24 in https://github.com/nf-core/spatialaxe/pull/156
• fix(modules): address awgymer review comments on PR #139 (strict nf-core compliance) by @an-altosian in https://github.com/nf-core/spatialaxe/pull/158
• fix: validate Xenium bundle after UNTAR (drop test-profile skip-validation guard) by @an-altosian in https://github.com/nf-core/spatialaxe/pull/159
• fix: address review comments on PR #139 by @heylf in https://github.com/nf-core/spatialaxe/pull/160
• Renaming pipeline into spatialaxe by @heylf in https://github.com/nf-core/spatialaxe/pull/162
• Just minor change to rename stuff in the svgs by @heylf in https://github.com/nf-core/spatialaxe/pull/171
• Adressing Kubras comments for release PR by @heylf in https://github.com/nf-core/spatialaxe/pull/172
• Release version 1.0.0 by @heylf in https://github.com/nf-core/spatialaxe/pull/139

New Contributors

• @heylf made their first contribution in https://github.com/nf-core/spatialaxe/pull/48
• @nf-core-bot made their first contribution in https://github.com/nf-core/spatialaxe/pull/50
• @kubranarci made their first contribution in https://github.com/nf-core/spatialaxe/pull/62
• @mcmero made their first contribution in https://github.com/nf-core/spatialaxe/pull/114
• @an-altosian made their first contribution in https://github.com/nf-core/spatialaxe/pull/123

Full Changelog: https://github.com/nf-core/spatialaxe/commits/1.0.0