From b05f01f851dd62cbe165bdaa938856e38e386e5b Mon Sep 17 00:00:00 2001 From: f641l Date: Thu, 6 Aug 2026 15:12:36 +0200 Subject: [PATCH 1/3] change to CHANGELOG.md --- CHANGELOG.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index e9f88b2..67f9bd0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -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 @@ -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` From b55e1ab94ac43126666fe0d2558d112c68564474 Mon Sep 17 00:00:00 2001 From: f641l Date: Thu, 6 Aug 2026 15:12:49 +0200 Subject: [PATCH 2/3] remove defualt outdir=results from tests --- conf/test.config | 1 - conf/test_full.config | 1 - conf/tests/test_coordinate_mode.config | 1 - conf/tests/test_image_mode.config | 1 - conf/tests/test_preview_mode.config | 1 - conf/tests/test_segfree_mode.config | 1 - 6 files changed, 6 deletions(-) diff --git a/conf/test.config b/conf/test.config index e317612..1784c30 100644 --- a/conf/test.config +++ b/conf/test.config @@ -30,6 +30,5 @@ params { // Input data input = "${projectDir}/assets/samplesheet.csv" - outdir = 'results' mode = 'coordinate' } diff --git a/conf/test_full.config b/conf/test_full.config index 68ce418..fc94c8f 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -16,6 +16,5 @@ params { // Input data input = "${projectDir}/assets/samplesheet.csv" - outdir = 'results' mode = 'coordinate' } diff --git a/conf/tests/test_coordinate_mode.config b/conf/tests/test_coordinate_mode.config index cccdae5..52b1f86 100644 --- a/conf/tests/test_coordinate_mode.config +++ b/conf/tests/test_coordinate_mode.config @@ -26,6 +26,5 @@ params { // Input data input = "${projectDir}/assets/samplesheet.csv" - outdir = 'results' mode = 'coordinate' } diff --git a/conf/tests/test_image_mode.config b/conf/tests/test_image_mode.config index ff9199d..987c68c 100644 --- a/conf/tests/test_image_mode.config +++ b/conf/tests/test_image_mode.config @@ -26,6 +26,5 @@ params { // Input data input = "${projectDir}/assets/samplesheet.csv" - outdir = 'results' mode = 'image' } diff --git a/conf/tests/test_preview_mode.config b/conf/tests/test_preview_mode.config index 5f31289..80bbf05 100644 --- a/conf/tests/test_preview_mode.config +++ b/conf/tests/test_preview_mode.config @@ -26,6 +26,5 @@ params { // Input data input = "${projectDir}/assets/samplesheet.csv" - outdir = 'results' mode = 'preview' } diff --git a/conf/tests/test_segfree_mode.config b/conf/tests/test_segfree_mode.config index 4576929..0ffa05e 100644 --- a/conf/tests/test_segfree_mode.config +++ b/conf/tests/test_segfree_mode.config @@ -26,6 +26,5 @@ params { // Input data input = "${projectDir}/assets/samplesheet.csv" - outdir = 'results' mode = 'segfree' } From a1def92c4c56d8a43fc0c3eea99363075f59067b Mon Sep 17 00:00:00 2001 From: f641l Date: Thu, 6 Aug 2026 15:13:01 +0200 Subject: [PATCH 3/3] slight change to usage.md --- docs/usage.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index 0252304..406f538 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -42,7 +42,7 @@ This runs the default image mode:
nextflow run nf-core/spatialaxe \ -profile --input ./samplesheet.csv \ - --outdir ./results \ + --outdir \ --mode image ``` @@ -55,7 +55,7 @@ This runs the default coordinate mode:
nextflow run nf-core/spatialaxe \ -profile --input ./samplesheet.csv \ - --outdir ./results \ + --outdir \ --mode coordinate ``` @@ -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 --input ./samplesheet.csv \ - --outdir ./results \ + --outdir \ --mode image \ --run_qc ``` @@ -136,7 +136,7 @@ eg: To run proseg segmentation use the `coordinate` mode and the `proseg` segmen nextflow run nf-core/spatialaxe \ -profile --input ./samplesheet.csv \ - --outdir ./results \ + --outdir \ --mode coordinate \ --method proseg ``` @@ -147,7 +147,7 @@ eg: To run cellpose segmentation use the `image` mode and the `cellpose` segment nextflow run nf-core/spatialaxe \ -profile --input ./samplesheet.csv \ - --outdir ./results \ + --outdir \ --mode image \ --method cellpose ```