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implement matthias recom, update to snaptshots and version bump. #194

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864be36
implement matthias recom, update to snaptshots and version bump.
heylf Jul 23, 2026
0d9cffc
prettier for Changelog and modules.json
heylf Jul 23, 2026
cb5d435
taken out stuff from CHANELOG
heylf Jul 23, 2026
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2 changes: 1 addition & 1 deletion CHANGELOG.md
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Expand Up @@ -3,7 +3,7 @@
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## 1.0.0dev - [date]
## 1.0.1 - [date]
Comment thread
mashehu marked this conversation as resolved.

Initial release of nf-core/spatialaxe, created with the [nf-core](https://nf-co.re/) template.

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2 changes: 1 addition & 1 deletion assets/multiqc_config.yml
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@@ -1,5 +1,5 @@
report_comment: >
This report has been generated by the <a href="https://github.com/nf-core/spatialaxe/tree/dev" target="_blank">nf-core/spatialaxe</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/spatialaxe/dev/docs/output" target="_blank">documentation</a>.
This report has been generated by the <a href="https://github.com/nf-core/spatialaxe/releases/tag/1.0.1" target="_blank">nf-core/spatialaxe</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/spatialaxe/1.0.1/docs/output" target="_blank">documentation</a>.
report_section_order:
"nf-core-spatialaxe-methods-description":
order: -1000
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7 changes: 0 additions & 7 deletions conf/modules.config
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Expand Up @@ -82,13 +82,6 @@ process {
path: "${params.outdir}/${params.mode}/xeniumranger/import_segementation",
mode: params.publish_dir_mode,
]
// --expansion-distance is only valid for nuclei-based imports (it expands nuclei
// into cell boundaries). xeniumranger rejects it for transcript-assignment imports
// (proseg/baysor/segger) and cells-only imports with "--expansion-distance requires
// --nuclei", so only emit it when a nuclei segmentation is being imported.
ext.args = {[
(nuclei && params.expansion_distance != null) ? "--expansion-distance=${params.expansion_distance}" : "",
].join(' ').trim()}
}

// ---------------------------- proseg ---------------------------------------------------
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7 changes: 6 additions & 1 deletion modules/nf-core/xeniumranger/import-segmentation/main.nf
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2 changes: 1 addition & 1 deletion nextflow.config
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Expand Up @@ -385,7 +385,7 @@ manifest {
mainScript = 'main.nf'
defaultBranch = 'master'
nextflowVersion = '!>=25.04.0'
version = '1.1.0dev'
version = '1.0.1'
doi = ''
}

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58 changes: 38 additions & 20 deletions ro-crate-metadata.json
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2 changes: 2 additions & 0 deletions subworkflows/local/baysor_run_prior_segmentation_mask/main.nf
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Expand Up @@ -18,6 +18,7 @@ workflow BAYSOR_RUN_PRIOR_SEGMENTATION_MASK {
min_qv // value: minimum transcript QV
min_x // value: spatial filter lower x bound
min_y // value: spatial filter lower y bound
expansion_distance // value: nuclear expansion distance

main:

Expand Down Expand Up @@ -69,6 +70,7 @@ workflow BAYSOR_RUN_PRIOR_SEGMENTATION_MASK {
polygons2d,
[],
ch_coordinate_space.val,
expansion_distance,
)
}
XENIUMRANGER_IMPORT_SEGMENTATION(
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7 changes: 5 additions & 2 deletions subworkflows/local/baysor_run_transcripts_parquet/main.nf
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Expand Up @@ -35,6 +35,7 @@ workflow BAYSOR_RUN_TRANSCRIPTS_PARQUET {
min_qv // value: minimum transcript QV
min_x // value: spatial filter lower x bound
min_y // value: spatial filter lower y bound
expansion_distance // value: nuclear expansion distance

main:

Expand Down Expand Up @@ -112,7 +113,8 @@ workflow BAYSOR_RUN_TRANSCRIPTS_PARQUET {
xr_transcript_metadata,
xr_cell_polygons,
[], [], [],
"microns"
"microns",
expansion_distance,
)
}

Expand Down Expand Up @@ -154,7 +156,8 @@ workflow BAYSOR_RUN_TRANSCRIPTS_PARQUET {
segmentation_csv,
polygons2d,
[], [], [],
ch_coordinate_space.val)
ch_coordinate_space.val,
expansion_distance)
}

XENIUMRANGER_IMPORT_SEGMENTATION(ch_xr)
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3 changes: 2 additions & 1 deletion subworkflows/local/baysor_run_transcripts_parquet_tiled/main.nf
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Expand Up @@ -19,6 +19,7 @@ workflow BAYSOR_RUN_TRANSCRIPTS_PARQUET_TILED {
min_qv // value: minimum transcript QV
min_x // value: spatial filter lower x bound
min_y // value: spatial filter lower y bound
expansion_distance // value: nuclear expansion distance

main:

Expand Down Expand Up @@ -93,7 +94,7 @@ workflow BAYSOR_RUN_TRANSCRIPTS_PARQUET_TILED {
.combine(XENIUM_PATCH_STITCH.out.xr_polygons_transcript, by: 0)
.combine(ch_coordinate_space)
.map { meta, bundle, geojson, csv, coord_space ->
tuple(meta, bundle, csv, geojson, [], [], [], coord_space)
tuple(meta, bundle, csv, geojson, [], [], [], coord_space, expansion_distance)
}

XENIUMRANGER_IMPORT_SEGMENTATION ( ch_xr )
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2 changes: 2 additions & 0 deletions subworkflows/local/cellpose_baysor_import_segmentation/main.nf
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Expand Up @@ -30,6 +30,7 @@ workflow CELLPOSE_BAYSOR_IMPORT_SEGMENTATION {
nucleus_segmentation_only // value: bool
sharpen_tiff // value: bool
stardist_nuclei_model // value: stardist pretrained model name
expansion_distance // value: nuclear expansion distance

main:

Expand Down Expand Up @@ -180,6 +181,7 @@ workflow CELLPOSE_BAYSOR_IMPORT_SEGMENTATION {
[],
[],
ch_coordinate_space.val,
expansion_distance,
)
}

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3 changes: 3 additions & 0 deletions subworkflows/local/cellpose_resolift_morphology_ome_tif/main.nf
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Expand Up @@ -20,6 +20,7 @@ workflow CELLPOSE_RESOLIFT_MORPHOLOGY_OME_TIF {
nucleus_segmentation_only // value: bool
sharpen_tiff // value: bool
stardist_nuclei_model // value: stardist pretrained model name
expansion_distance // value: nuclear expansion distance

main:

Expand Down Expand Up @@ -106,6 +107,7 @@ workflow CELLPOSE_RESOLIFT_MORPHOLOGY_OME_TIF {
[],
[],
coord_space,
expansion_distance,
)
}
XENIUMRANGER_IMPORT_SEGMENTATION(
Expand All @@ -128,6 +130,7 @@ workflow CELLPOSE_RESOLIFT_MORPHOLOGY_OME_TIF {
cells_seg,
[],
coord_space,
expansion_distance,
)
}
XENIUMRANGER_IMPORT_SEGMENTATION(
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2 changes: 2 additions & 0 deletions subworkflows/local/proseg_preset_proseg2baysor/main.nf
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Expand Up @@ -10,6 +10,7 @@ workflow PROSEG_PRESET_PROSEG2BAYSOR {
take:
ch_bundle_path // channel: [ val(meta), ["path-to-xenium-bundle"] ]
ch_transcripts_file // channel: [ val(meta), [ "transcripts.parquet" ] ]
expansion_distance // value: nuclear expansion distance

main:

Expand Down Expand Up @@ -37,6 +38,7 @@ workflow PROSEG_PRESET_PROSEG2BAYSOR {
[],
[],
ch_coordinate_space.val,
expansion_distance,
)
}

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3 changes: 2 additions & 1 deletion subworkflows/local/proseg_preset_proseg2baysor_tiled/main.nf
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Expand Up @@ -13,6 +13,7 @@ workflow PROSEG_PRESET_PROSEG2BAYSOR_TILED {
take:
ch_bundle_path // channel: [ val(meta), ["path-to-xenium-bundle"] ]
ch_transcripts_file // channel: [ val(meta), [ "transcripts.parquet" ] ]
expansion_distance // value: nuclear expansion distance

main:

Expand Down Expand Up @@ -75,7 +76,7 @@ workflow PROSEG_PRESET_PROSEG2BAYSOR_TILED {
.combine(XENIUM_PATCH_STITCH.out.xr_polygons_transcript, by: 0)
.combine(ch_coordinate_space)
.map { meta, bundle, geojson, csv, coord_space ->
tuple(meta, bundle, csv, geojson, [], [], [], coord_space)
tuple(meta, bundle, csv, geojson, [], [], [], coord_space, expansion_distance)
}

XENIUMRANGER_IMPORT_SEGMENTATION ( ch_xr )
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2 changes: 2 additions & 0 deletions subworkflows/local/segger_create_train_predict/main.nf
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Expand Up @@ -13,6 +13,7 @@ workflow SEGGER_CREATE_TRAIN_PREDICT {
ch_bundle // channel: [ val(meta), ["path-to-xenium-bundle"] ]
ch_transcripts_file // channel: [ val(meta), [bundle + "/transcripts.parquet"]]
segger_model // value: path to a pre-trained segger model checkpoint (or null)
expansion_distance // value: nuclear expansion distance

main:

Expand Down Expand Up @@ -64,6 +65,7 @@ workflow SEGGER_CREATE_TRAIN_PREDICT {
[], // cells
[], // coordinate_transform
ch_coordinate_space.val,
expansion_distance,
)
}

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2 changes: 2 additions & 0 deletions subworkflows/local/stardist_resolift_morphology_ome_tif/main.nf
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Expand Up @@ -14,6 +14,7 @@ workflow STARDIST_RESOLIFT_MORPHOLOGY_OME_TIF {
ch_bundle_path // channel: [ val(meta), ["path-to-xenium-bundle"] ]
sharpen_tiff // value: bool
stardist_nuclei_model // value: stardist pretrained model name
expansion_distance // value: nuclear expansion distance

main:

Expand Down Expand Up @@ -58,6 +59,7 @@ workflow STARDIST_RESOLIFT_MORPHOLOGY_OME_TIF {
[],
[],
ch_coordinate_space.val,
expansion_distance,
)
}
XENIUMRANGER_IMPORT_SEGMENTATION(
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4 changes: 4 additions & 0 deletions subworkflows/local/xeniumranger_import_segmentation_redefine_bundle/main.nf
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Expand Up @@ -40,6 +40,7 @@ workflow XENIUMRANGER_IMPORT_SEGMENTATION_REDEFINE_BUNDLE {
[],
[],
ch_coordinate_space.val,
expansion_distance,
)
}

Expand All @@ -65,6 +66,7 @@ workflow XENIUMRANGER_IMPORT_SEGMENTATION_REDEFINE_BUNDLE {
[],
[],
ch_coordinate_space.val,
expansion_distance,
)
}

Expand All @@ -88,6 +90,7 @@ workflow XENIUMRANGER_IMPORT_SEGMENTATION_REDEFINE_BUNDLE {
polygons_geojson,
[],
ch_coordinate_space.val,
expansion_distance,
)
}

Expand Down Expand Up @@ -117,6 +120,7 @@ workflow XENIUMRANGER_IMPORT_SEGMENTATION_REDEFINE_BUNDLE {
polygons_geojson,
alignment_csv_file,
ch_coordinate_space.val,
expansion_distance,
)
}

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2 changes: 2 additions & 0 deletions subworkflows/local/xeniumranger_resegment_morphology_ome_tif/main.nf
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Expand Up @@ -9,6 +9,7 @@ workflow XENIUMRANGER_RESEGMENT_MORPHOLOGY_OME_TIF {
take:
ch_bundle_path // channel: [ val(meta), ["path-to-xenium-bundle"] ]
nucleus_segmentation_only // value: bool
expansion_distance // value: nuclear expansion distance

main:

Expand Down Expand Up @@ -41,6 +42,7 @@ workflow XENIUMRANGER_RESEGMENT_MORPHOLOGY_OME_TIF {
cells_zarr,
[],
"pixels",
expansion_distance,
)
}

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6 changes: 3 additions & 3 deletions tests/coordinate_mode.nf.test.snap
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Expand Up @@ -24,7 +24,7 @@
"untar": 1.34
},
"Workflow": {
"nf-core/spatialaxe": "v1.1.0dev"
"nf-core/spatialaxe": "v1.0.1"
},
"XENIUMRANGER_IMPORT_SEGMENTATION": {
"xeniumranger": "4.0.1.1"
Expand Down Expand Up @@ -143,10 +143,10 @@
"experiment.xenium:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"timestamp": "2026-05-18T21:58:08.945192717",
"timestamp": "2026-07-23T15:40:58.675984128",
"meta": {
"nf-test": "0.9.5",
"nextflow": "25.10.4"
"nextflow": "26.04.6"
}
}
}
6 changes: 3 additions & 3 deletions tests/default.nf.test.snap
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Expand Up @@ -24,7 +24,7 @@
"untar": 1.34
},
"Workflow": {
"nf-core/spatialaxe": "v1.1.0dev"
"nf-core/spatialaxe": "v1.0.1"
},
"XENIUMRANGER_IMPORT_SEGMENTATION": {
"xeniumranger": "4.0.1.1"
Expand Down Expand Up @@ -143,10 +143,10 @@
"experiment.xenium:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"timestamp": "2026-05-18T21:55:37.544217665",
"timestamp": "2026-07-23T15:44:34.596126547",
"meta": {
"nf-test": "0.9.5",
"nextflow": "25.10.4"
"nextflow": "26.04.6"
}
}
}
6 changes: 3 additions & 3 deletions tests/image_mode.nf.test.snap
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Expand Up @@ -30,7 +30,7 @@
"untar": 1.34
},
"Workflow": {
"nf-core/spatialaxe": "v1.1.0dev"
"nf-core/spatialaxe": "v1.0.1"
},
"XENIUMRANGER_IMPORT_SEGMENTATION": {
"xeniumranger": "4.0.1.1"
Expand Down Expand Up @@ -158,10 +158,10 @@
"resized_morphology_focus_0000.ome_cp_masks.tif.tif:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"timestamp": "2026-05-18T22:00:39.030306506",
"timestamp": "2026-07-23T15:56:50.983450195",
"meta": {
"nf-test": "0.9.5",
"nextflow": "25.10.4"
"nextflow": "26.04.6"
}
}
}
6 changes: 3 additions & 3 deletions tests/preview_mode.nf.test.snap
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Expand Up @@ -18,7 +18,7 @@
"untar": 1.34
},
"Workflow": {
"nf-core/spatialaxe": "v1.1.0dev"
"nf-core/spatialaxe": "v1.0.1"
}
},
[
Expand Down Expand Up @@ -111,10 +111,10 @@
"umap_mqc.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"timestamp": "2026-06-17T11:15:30.764424637",
"timestamp": "2026-07-23T15:57:29.316600844",
"meta": {
"nf-test": "0.9.5",
"nextflow": "26.04.2"
"nextflow": "26.04.6"
}
}
}
6 changes: 3 additions & 3 deletions tests/segfree_mode.nf.test.snap
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Expand Up @@ -12,7 +12,7 @@
"untar": 1.34
},
"Workflow": {
"nf-core/spatialaxe": "v1.1.0dev"
"nf-core/spatialaxe": "v1.0.1"
}
},
[
Expand Down Expand Up @@ -88,10 +88,10 @@
"transcripts.zarr.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"timestamp": "2026-05-18T22:02:39.947804998",
"timestamp": "2026-07-23T15:57:58.134363385",
"meta": {
"nf-test": "0.9.5",
"nextflow": "25.10.4"
"nextflow": "26.04.6"
}
}
}
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