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Merged
heylf merged 3 commits into from
Aug 6, 2026
Merged

Implementing revision for hotfix 1.0.1 #203

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b05f01f
change to CHANGELOG.md
heylf Aug 6, 2026
b55e1ab
remove defualt outdir=results from tests
heylf Aug 6, 2026
a1def92
slight change to usage.md
heylf Aug 6, 2026
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3 changes: 2 additions & 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).

## 1.0.1 - [31.07.2026]
## 1.0.1 - [06.08.2026]

Hotfix to tackle some bugs

Expand All @@ -12,6 +12,7 @@ Hotfix to tackle some bugs
- Template update for nf-core/tools version 4.0.3
- Adding new conf/tests folder
- Adding new test for coordinate mode to check the bugfixes
- Remove default outdir='results' for test profiles (tests)

### `Fixed`

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1 change: 0 additions & 1 deletion conf/test.config
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Expand Up @@ -30,6 +30,5 @@ params {

// Input data
input = "${projectDir}/assets/samplesheet.csv"
outdir = 'results'
mode = 'coordinate'
}
1 change: 0 additions & 1 deletion conf/test_full.config
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Expand Up @@ -16,6 +16,5 @@ params {

// Input data
input = "${projectDir}/assets/samplesheet.csv"
outdir = 'results'
mode = 'coordinate'
}
1 change: 0 additions & 1 deletion conf/tests/test_coordinate_mode.config
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Expand Up @@ -26,6 +26,5 @@ params {

// Input data
input = "${projectDir}/assets/samplesheet.csv"
outdir = 'results'
mode = 'coordinate'
}
1 change: 0 additions & 1 deletion conf/tests/test_image_mode.config
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Expand Up @@ -26,6 +26,5 @@ params {

// Input data
input = "${projectDir}/assets/samplesheet.csv"
outdir = 'results'
mode = 'image'
}
1 change: 0 additions & 1 deletion conf/tests/test_preview_mode.config
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Expand Up @@ -26,6 +26,5 @@ params {

// Input data
input = "${projectDir}/assets/samplesheet.csv"
outdir = 'results'
mode = 'preview'
}
1 change: 0 additions & 1 deletion conf/tests/test_segfree_mode.config
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Expand Up @@ -26,6 +26,5 @@ params {

// Input data
input = "${projectDir}/assets/samplesheet.csv"
outdir = 'results'
mode = 'segfree'
}
10 changes: 5 additions & 5 deletions docs/usage.md
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Expand Up @@ -42,7 +42,7 @@ This runs the default image mode:<br>
nextflow run nf-core/spatialaxe \
-profile <docker/singularity/...>
--input ./samplesheet.csv \
--outdir ./results \
--outdir <OUTDIR> \
--mode image
```

Expand All @@ -55,7 +55,7 @@ This runs the default coordinate mode:<br>
nextflow run nf-core/spatialaxe \
-profile <docker/singularity/...>
--input ./samplesheet.csv \
--outdir ./results \
--outdir <OUTDIR> \
--mode coordinate
```

Expand Down Expand Up @@ -91,7 +91,7 @@ It is possible to run the quality control with `--run_qc` to couple it with anot
nextflow run nf-core/spatialaxe \
-profile <docker/singularity/...>
--input ./samplesheet.csv \
--outdir ./results \
--outdir <OUTDIR> \
--mode image \
--run_qc
```
Expand Down Expand Up @@ -136,7 +136,7 @@ eg: To run proseg segmentation use the `coordinate` mode and the `proseg` segmen
nextflow run nf-core/spatialaxe \
-profile <docker/singularity/...>
--input ./samplesheet.csv \
--outdir ./results \
--outdir <OUTDIR> \
--mode coordinate \
--method proseg
```
Expand All @@ -147,7 +147,7 @@ eg: To run cellpose segmentation use the `image` mode and the `cellpose` segment
nextflow run nf-core/spatialaxe \
-profile <docker/singularity/...>
--input ./samplesheet.csv \
--outdir ./results \
--outdir <OUTDIR> \
--mode image \
--method cellpose
```
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