nf-core · heylf · May 7, 2026 · May 5, 2026 · May 5, 2026 · May 7, 2026
diff --git a/modules/local/baysor/create_dataset/main.nf b/modules/local/baysor/create_dataset/main.nf
@@ -24,7 +24,7 @@ process BAYSOR_CREATE_DATASET {
     prefix = task.ext.prefix ?: "${meta.id}"
 
     """
-    create_dataset.py \\
+    python3 ${moduleDir}/templates/create_dataset.py \\
         --transcripts ${transcripts} \\
         --sample-fraction ${sample_fraction} \\
         --prefix ${prefix}

diff --git a/...taset/resources/usr/bin/create_dataset.py → ...reate_dataset/templates/create_dataset.py b/...taset/resources/usr/bin/create_dataset.py → ...reate_dataset/templates/create_dataset.py
diff --git a/modules/local/baysor/preprocess/main.nf b/modules/local/baysor/preprocess/main.nf
@@ -30,7 +30,7 @@ process BAYSOR_PREPROCESS_TRANSCRIPTS {
     prefix = task.ext.prefix ?: "${meta.id}"
 
     """
-    preprocess_transcripts.py \\
+    python3 ${moduleDir}/templates/preprocess_transcripts.py \\
         --transcripts ${transcripts} \\
         --prefix ${prefix} \\
         --min-qv ${min_qv} \\

diff --git a/...sources/usr/bin/preprocess_transcripts.py → ...ocess/templates/preprocess_transcripts.py b/...sources/usr/bin/preprocess_transcripts.py → ...ocess/templates/preprocess_transcripts.py
diff --git a/modules/local/ficture/preprocess/main.nf b/modules/local/ficture/preprocess/main.nf
@@ -24,7 +24,7 @@ process FICTURE_PREPROCESS {
     def features_arg = features ? "--features ${features}" : ""
 
     """
-    ficture_preprocess.py \\
+    python3 ${moduleDir}/templates/ficture_preprocess.py \\
         --transcripts ${transcripts} \\
         ${features_arg} \\
         --negative-control-regex '${params.negative_control_regex}' \\

diff --git a/...s/resources/usr/bin/ficture_preprocess.py → ...reprocess/templates/ficture_preprocess.py b/...s/resources/usr/bin/ficture_preprocess.py → ...reprocess/templates/ficture_preprocess.py
diff --git a/modules/local/segger/create_dataset/main.nf b/modules/local/segger/create_dataset/main.nf
@@ -33,7 +33,7 @@ process SEGGER_CREATE_DATASET {
     export NUMBA_CACHE_DIR=\$PWD/.numba_cache
     mkdir -p \$NUMBA_CACHE_DIR
 
-    run_create_dataset.py \\
+    python3 ${moduleDir}/templates/run_create_dataset.py \\
         --bundle-dir ${base_dir} \\
         --output-dir ${prefix} \\
         --sample-type ${params.format} \\

diff --git a/...t/resources/usr/bin/run_create_dataset.py → ...e_dataset/templates/run_create_dataset.py b/...t/resources/usr/bin/run_create_dataset.py → ...e_dataset/templates/run_create_dataset.py
diff --git a/modules/local/segger/predict/main.nf b/modules/local/segger/predict/main.nf
@@ -27,7 +27,7 @@ process SEGGER_PREDICT {
     def args = task.ext.args ?: ''
     prefix = task.ext.prefix ?: "${meta.id}"
     """
-    run_predict.py \\
+    python3 ${moduleDir}/templates/run_predict.py \\
         --models-dir ${models_dir} \\
         --segger-data-dir ${segger_dataset} \\
         --transcripts-file ${transcripts} \\

diff --git a/.../predict/resources/usr/bin/run_predict.py → ...l/segger/predict/templates/run_predict.py b/.../predict/resources/usr/bin/run_predict.py → ...l/segger/predict/templates/run_predict.py
diff --git a/modules/local/spatialdata/merge/main.nf b/modules/local/spatialdata/merge/main.nf
@@ -26,7 +26,7 @@ process SPATIALDATA_MERGE {
     prefix = task.ext.prefix ?: "${meta.id}"
 
     """
-    spatialdata_merge.py \\
+    python3 ${moduleDir}/templates/spatialdata_merge.py \\
         --raw-bundle ${raw_bundle} \\
         --redefined-bundle ${redefined_bundle} \\
         --prefix ${prefix} \\

diff --git a/...ge/resources/usr/bin/spatialdata_merge.py → ...data/merge/templates/spatialdata_merge.py b/...ge/resources/usr/bin/spatialdata_merge.py → ...data/merge/templates/spatialdata_merge.py
diff --git a/modules/local/spatialdata/meta/main.nf b/modules/local/spatialdata/meta/main.nf
@@ -26,7 +26,7 @@ process SPATIALDATA_META {
     prefix = task.ext.prefix ?: "${meta.id}"
 
     """
-    spatialdata_meta.py \\
+    python3 ${moduleDir}/templates/spatialdata_meta.py \\
         --spatialdata-bundle ${spatialdata_bundle} \\
         --xenium-bundle ${xenium_bundle} \\
         --prefix ${prefix} \\

diff --git a/...eta/resources/usr/bin/spatialdata_meta.py → ...aldata/meta/templates/spatialdata_meta.py b/...eta/resources/usr/bin/spatialdata_meta.py → ...aldata/meta/templates/spatialdata_meta.py
diff --git a/modules/local/spatialdata/write/main.nf b/modules/local/spatialdata/write/main.nf
@@ -28,7 +28,7 @@ process SPATIALDATA_WRITE {
     prefix = task.ext.prefix ?: "${meta.id}"
 
     """
-    spatialdata_write.py \\
+    python3 ${moduleDir}/templates/spatialdata_write.py \\
         --bundle ${bundle} \\
         --prefix ${prefix} \\
         --output-folder ${outputfolder} \\

diff --git a/...te/resources/usr/bin/spatialdata_write.py → ...data/write/templates/spatialdata_write.py b/...te/resources/usr/bin/spatialdata_write.py → ...data/write/templates/spatialdata_write.py
diff --git a/modules/local/utility/convert_mask_uint32/main.nf b/modules/local/utility/convert_mask_uint32/main.nf
@@ -35,7 +35,7 @@ process CONVERT_MASK_UINT32 {
     script:
     prefix = task.ext.prefix ?: "${meta.id}"
     """
-    convert_mask_uint32.py \\
+    python3 ${moduleDir}/templates/convert_mask_uint32.py \\
         --input ${mask} \\
         --output ${prefix}_uint32_mask.tif
     """

diff --git a/.../resources/usr/bin/convert_mask_uint32.py → ...k_uint32/templates/convert_mask_uint32.py b/.../resources/usr/bin/convert_mask_uint32.py → ...k_uint32/templates/convert_mask_uint32.py
diff --git a/modules/local/utility/downscale_morphology/main.nf b/modules/local/utility/downscale_morphology/main.nf
@@ -41,7 +41,7 @@ process DOWNSCALE_MORPHOLOGY {
     def diam_mean = 30
     prefix = task.ext.prefix ?: "${meta.id}"
     """
-    downscale_morphology.py \\
+    python3 ${moduleDir}/templates/downscale_morphology.py \\
         --image ${image} \\
         --diameter ${diameter} \\
         --diam-mean ${diam_mean} \\

diff --git a/...resources/usr/bin/downscale_morphology.py → ...phology/templates/downscale_morphology.py b/...resources/usr/bin/downscale_morphology.py → ...phology/templates/downscale_morphology.py
diff --git a/modules/local/utility/extract_dapi/main.nf b/modules/local/utility/extract_dapi/main.nf
@@ -36,7 +36,7 @@ process EXTRACT_DAPI {
     prefix = task.ext.prefix ?: "${meta.id}"
     def channel_index = task.ext.channel_index ?: 0
     """
-    extract_dapi.py \\
+    python3 ${moduleDir}/templates/extract_dapi.py \\
         --input ${image} \\
         --output ${prefix}_dapi.tif \\
         --channel-index ${channel_index}

diff --git a/...ct_dapi/resources/usr/bin/extract_dapi.py → ...ty/extract_dapi/templates/extract_dapi.py b/...ct_dapi/resources/usr/bin/extract_dapi.py → ...ty/extract_dapi/templates/extract_dapi.py
diff --git a/modules/local/utility/extract_preview_data/main.nf b/modules/local/utility/extract_preview_data/main.nf
@@ -26,7 +26,7 @@ process EXTRACT_PREVIEW_DATA {
     prefix = task.ext.prefix ?: "${meta.id}"
 
     """
-    extract_data.py \\
+    python3 ${moduleDir}/templates/extract_data.py \\
         --preview-html ${preview_html} \\
         --prefix ${prefix}
     """

diff --git a/...ew_data/resources/usr/bin/extract_data.py → ...ct_preview_data/templates/extract_data.py b/...ew_data/resources/usr/bin/extract_data.py → ...ct_preview_data/templates/extract_data.py
diff --git a/modules/local/utility/get_coordinates/main.nf b/modules/local/utility/get_coordinates/main.nf
@@ -25,7 +25,7 @@ process GET_TRANSCRIPTS_COORDINATES {
     prefix = task.ext.prefix ?: "${meta.id}"
 
     """
-    get_coordinates.py \\
+    python3 ${moduleDir}/templates/get_coordinates.py \\
         --transcripts ${transcripts}
     """
 

diff --git a/...ates/resources/usr/bin/get_coordinates.py → ..._coordinates/templates/get_coordinates.py b/...ates/resources/usr/bin/get_coordinates.py → ..._coordinates/templates/get_coordinates.py
diff --git a/modules/local/utility/parquet_to_csv/main.nf b/modules/local/utility/parquet_to_csv/main.nf
@@ -25,7 +25,7 @@ process PARQUET_TO_CSV {
     prefix = task.ext.prefix ?: "${meta.id}"
 
     """
-    parquet_to_csv.py \\
+    python3 ${moduleDir}/templates/parquet_to_csv.py \\
         --transcripts ${transcripts} \\
         --extension ${extension} \\
         --prefix ${prefix}

diff --git a/...o_csv/resources/usr/bin/parquet_to_csv.py → ...arquet_to_csv/templates/parquet_to_csv.py b/...o_csv/resources/usr/bin/parquet_to_csv.py → ...arquet_to_csv/templates/parquet_to_csv.py
diff --git a/modules/local/utility/resize_tif/main.nf b/modules/local/utility/resize_tif/main.nf
@@ -26,7 +26,7 @@ process RESIZE_TIF {
     prefix = task.ext.prefix ?: "${meta.id}"
 
     """
-    resize_tif.py \\
+    python3 ${moduleDir}/templates/resize_tif.py \\
         --mask ${mask} \\
         --transcripts ${transcripts} \\
         --metadata ${metadata} \\

diff --git a/...esize_tif/resources/usr/bin/resize_tif.py → ...tility/resize_tif/templates/resize_tif.py b/...esize_tif/resources/usr/bin/resize_tif.py → ...tility/resize_tif/templates/resize_tif.py
diff --git a/modules/local/utility/segger2xr/main.nf b/modules/local/utility/segger2xr/main.nf
@@ -27,7 +27,7 @@ process SEGGER2XR {
     def min_transcripts = task.ext.min_transcripts_per_cell ?: 3
 
     """
-    segger2xr.py \\
+    python3 ${moduleDir}/templates/segger2xr.py \\
         --transcripts ${transcripts} \\
         --prefix ${meta.id} \\
         --min-transcripts ${min_transcripts}

diff --git a/.../segger2xr/resources/usr/bin/segger2xr.py → .../utility/segger2xr/templates/segger2xr.py b/.../segger2xr/resources/usr/bin/segger2xr.py → .../utility/segger2xr/templates/segger2xr.py
diff --git a/modules/local/utility/split_transcripts/main.nf b/modules/local/utility/split_transcripts/main.nf
@@ -26,7 +26,7 @@ process SPLIT_TRANSCRIPTS {
     def prefix = task.ext.prefix ?: "${meta.id}"
 
     """
-    split_transcripts.py \\
+    python3 ${moduleDir}/templates/split_transcripts.py \\
         --transcripts ${transcripts} \\
         --x-bins ${x_bins} \\
         --y-bins ${y_bins} \\

diff --git a/...ts/resources/usr/bin/split_transcripts.py → ...ranscripts/templates/split_transcripts.py b/...ts/resources/usr/bin/split_transcripts.py → ...ranscripts/templates/split_transcripts.py
diff --git a/modules/local/utility/upscale_mask/main.nf b/modules/local/utility/upscale_mask/main.nf
@@ -35,7 +35,7 @@ process UPSCALE_MASK {
     script:
     prefix = task.ext.prefix ?: "${meta.id}"
     """
-    upscale_mask.py \\
+    python3 ${moduleDir}/templates/upscale_mask.py \\
         --mask ${mask} \\
         --scale-info ${scale_info} \\
         --prefix ${prefix}

diff --git a/...le_mask/resources/usr/bin/upscale_mask.py → ...ty/upscale_mask/templates/upscale_mask.py b/...le_mask/resources/usr/bin/upscale_mask.py → ...ty/upscale_mask/templates/upscale_mask.py
diff --git a/modules/local/xenium_patch/stitch/main.nf b/modules/local/xenium_patch/stitch/main.nf
@@ -35,14 +35,14 @@ process XENIUM_PATCH_STITCH {
     script:
     def args = task.ext.args ?: ''
     """
-    stitch_transcripts.py \\
+    python3 ${moduleDir}/templates/stitch_transcripts.py \\
         --patches ${patches} \\
         --output output \\
         ${args}
 
     # Post-process: ensure all GeoJSON geometries are Polygon and
     # reconcile dropped cells in the transcript CSV.
-    stitch_postprocess.py \\
+    python3 ${moduleDir}/templates/stitch_postprocess.py \\
         --geojson output/xr-cell-polygons.geojson \\
         --csv output/xr-transcript-metadata.csv
     """

diff --git a/...h/resources/usr/bin/stitch_postprocess.py → ...ch/stitch/templates/stitch_postprocess.py b/...h/resources/usr/bin/stitch_postprocess.py → ...ch/stitch/templates/stitch_postprocess.py
diff --git a/...h/resources/usr/bin/stitch_transcripts.py → ...ch/stitch/templates/stitch_transcripts.py b/...h/resources/usr/bin/stitch_transcripts.py → ...ch/stitch/templates/stitch_transcripts.py