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Important! Template update for nf-core/tools v3.3.2
Massive linting fixes and other minor changes
Added new module and subworkflow for opt, Ci fix changes
Multisample support for spatialxe runs
Testing changes and code formatting
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Renaming of the pipeline is complete |
an-altosian
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May 28, 2026
Bug 2 from the Atera compatibility report: 19 modules using
python3 ${moduleDir}/templates/<script>.py
fail on Tower / AWS Batch with
python3: can't open file '/.nextflow/assets/an-altosian/spatialaxe/modules/local/<x>/templates/<script>.py': [Errno 2] No such file or directory
because ${moduleDir} interpolates the head-node path into .command.sh,
but the templates aren't staged at that absolute path on AWS Batch
workers. The path resolves to /.nextflow/... (leading slash) because
HOME is empty inside the worker container.
This regressed in PR nf-core#154 (commits 4f21dd2 -> ea46ad0 -> dbd7a35) which
moved the scripts from bin/ into per-module templates/ folders to
satisfy PR nf-core#139's no-module-level-bin review. The follow-up dbd7a35
switched from the 'template <file>.py' directive (which broke eval() in
non-Bash interpreters) to the shell-call invocation above -- which
works in local nf-test but breaks on Tower.
Fix: move the 20 scripts from modules/local/<x>/templates/ back to the
top-level bin/ directory, and invoke them by name. Nextflow auto-adds
bin/ to PATH on workers, so this works on Tower (and matches the
nf-core canonical pattern used by most pipelines). PR nf-core#139's review was
specifically about MODULE-level bin (modules/local/<x>/bin/) -- top-level
bin/ remains permissible.
Also cleans up 3 pre-existing unused imports in spatialdata_{merge,meta,write}.py
that ruff flagged once the scripts moved into the linted bin/ path.
Affected (19 modules, 20 scripts):
- baysor/{create_dataset,preprocess}
- ficture/preprocess
- segger/{create_dataset,predict}
- spatialdata/{merge,meta,write}
- utility/{convert_mask_uint32,downscale_morphology,extract_dapi,
extract_preview_data,get_coordinates,parquet_to_csv,
resize_tif,segger2xr,split_transcripts,upscale_mask}
- xenium_patch/stitch (2 scripts: stitch_transcripts + stitch_postprocess)
The orphaned pre-refactor bin/stitch_transcripts.py is overwritten by
the canonical templates/ version (sopa-based solve_conflicts() impl).
awgymer
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Jun 2, 2026
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Do these need to be changed:
docs/images/spatialaxe-logo.svg:10: sodipodi:docname="spatialxe-logo.svg"
docs/images/spatialaxe-logo.svg:12: inkscape:export-filename="spatialxe-logo.png"
docs/images/spatialaxe-metromap.svg:12: sodipodi:docname="spatialxe-metromap.svg"
docs/images/spatialaxe-metromap.svg:13: inkscape:export-filename="spatialxe-metromap.png"
Just minor change to rename stuff in the svgs
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Fixed the issues commented before |
awgymer
approved these changes
Jun 15, 2026
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You still need a 2nd approving review from someone else who hasn't worked on the code. |
kubranarci
reviewed
Jun 16, 2026
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I see that in many of the local modules and subworkflows, the topic migration is done for main.nf yet meta.yml is not updated accordingly.
Adressing Kubras comments for release PR
kubranarci
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Jun 17, 2026
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Congrats over your first release!
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The first release version of spatialxe. During the developemnt many tools were debugged, and new tools were added.
Since it is a first release thorough review is required.
PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).