nf-core · heylf · Apr 30, 2026 · Apr 30, 2026 · Apr 30, 2026 · Apr 30, 2026
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
@@ -24,7 +24,6 @@ jobs:
 
       - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
-        # TODO nf-core: You can customise AWS full pipeline tests as required
         # Add full size test data (but still relatively small datasets for few samples)
         # on the `test_full.config` test runs with only one set of parameters
         with:

diff --git a/.nf-core.yml b/.nf-core.yml
@@ -12,11 +12,13 @@ lint:
 nf_core_version: 3.5.2
 repository_type: pipeline
 template:
-  author: Sameesh Kher, Florian Heyl
+  author: Sameesh Kher, Dongze He, Florian Heyl
   description: A pipeline for spatialomics Xenium In Situ data.
   force: false
   is_nfcore: true
   name: spatialxe
   org: nf-core
   outdir: .
+  skip_features:
+    - igenomes
   version: 1.0.0
diff --git a/README.md b/README.md
@@ -181,11 +181,8 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
 
 ## Citations
 
-<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
 <!-- If you use nf-core/spatialxe for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
 
-<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
-
 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
 
 You can cite the `nf-core` publication as follows:

diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml
@@ -3,7 +3,6 @@ description: "Suggested text and references to use when describing pipeline usag
 section_name: "nf-core/spatialxe Methods Description"
 section_href: "https://github.com/nf-core/spatialxe"
 plot_type: "html"
-## nf-core: Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
 ## You inject any metadata in the Nextflow '${workflow}' object
 data: |
   <h4>Methods</h4>

diff --git a/conf/base.config b/conf/base.config
@@ -14,7 +14,7 @@ process {
     memory = { 6.GB * task.attempt }
     time   = { 4.h  * task.attempt }
 
-    resourceLimits = [ cpus: 192, memory: 750.GB, time: 72.h ]
+    // resourceLimits = [ cpus: 192, memory: 750.GB, time: 72.h ]
 
     errorStrategy = { task.exitStatus in ((130..145) + 104 + 2147483647) ? 'retry' : 'finish' }
     maxRetries    = 3
@@ -79,7 +79,7 @@ process {
     withLabel:process_gpu {
         ext.use_gpu = { params.use_gpu }
         accelerator = { params.use_gpu ? 1 : null }
-        containerOptions = { "--shm-size ${task.memory.toGiga().intValue()}g" }
+        // containerOptions = { "--shm-size ${task.memory.toGiga().intValue()}g" }
     }
 
     // Single-GPU processes (e.g., Cellpose, StarDist)

diff --git a/conf/modules.config b/conf/modules.config
@@ -218,7 +218,7 @@ process {
 
     withName: PARQUET_TO_CSV {
         publishDir = [
-            path: { "${params.outdir}/${params.mode}/utility/spatialconverter/parquet_to_csv" },
+            path: { "${params.outdir}/${params.mode}/utility/parquet_to_csv" },
             mode: params.publish_dir_mode,
         ]
     }

diff --git a/conf/test_coordinate_mode.config b/conf/test_coordinate_mode.config
@@ -21,7 +21,7 @@ process {
 }
 
 params {
-    config_profile_name        = 'Test profile'
+    config_profile_name        = 'Test profile coordinate mode'
     config_profile_description = 'Minimal test dataset to check pipeline function in the coordinate mode'
 
     // Input data

diff --git a/conf/test_image_mode.config b/conf/test_image_mode.config
@@ -21,7 +21,7 @@ process {
 }
 
 params {
-    config_profile_name        = 'Test profile'
+    config_profile_name        = 'Test profile image mode'
     config_profile_description = 'Minimal test dataset to check pipeline function in the image mode'
 
     // Input data

diff --git a/conf/test_preview_mode.config b/conf/test_preview_mode.config
@@ -21,7 +21,7 @@ process {
 }
 
 params {
-    config_profile_name        = 'Test profile'
+    config_profile_name        = 'Test profile preview mode'
     config_profile_description = 'Minimal test dataset to check pipeline function in the preview mode'
 
     // Input data

diff --git a/conf/test_segfree_mode.config b/conf/test_segfree_mode.config
@@ -21,7 +21,7 @@ process {
 }
 
 params {
-    config_profile_name        = 'Test profile'
+    config_profile_name        = 'Test profile segfree mode'
     config_profile_description = 'Minimal test dataset to check pipeline function in the segfree mode'
 
     // Input data

diff --git a/modules/local/baysor/create_dataset/tests/main.nf.test b/modules/local/baysor/create_dataset/tests/main.nf.test
@@ -15,7 +15,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.of([
+                input[0] = channel.of([
                                 [id: "test_run_baysor"],
                                 file(params.modules_testdata_base_path + "spatial_omics/xenium/homo_sapiens/spatial_gene_expression.csv", checkIfExists: true)
                             ])
@@ -41,7 +41,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.of([
+                input[0] = channel.of([
                                 [id: "test_run_baysor"],
                                 file(params.modules_testdata_base_path + "spatial_omics/xenium/homo_sapiens/spatial_gene_expression.csv", checkIfExists: true)
                             ])

diff --git a/modules/local/baysor/preprocess/tests/main.nf.test b/modules/local/baysor/preprocess/tests/main.nf.test
@@ -15,7 +15,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.of([
+                input[0] = channel.of([
                                 [id: "test_run_baysor"],
                                 file("https://raw.githubusercontent.com/khersameesh24/test-datasets/baysor/transcripts.parquet", checkIfExists: true)
                             ])
@@ -45,7 +45,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.of([
+                input[0] = channel.of([
                                 [id: "test_run_baysor"],
                                 file("https://raw.githubusercontent.com/khersameesh24/test-datasets/baysor/transcripts.parquet", checkIfExists: true)
                             ])

diff --git a/modules/local/baysor/preview/tests/main.nf.test b/modules/local/baysor/preview/tests/main.nf.test
@@ -15,7 +15,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.of([
+                input[0] = channel.of([
                                 [id: "test_run_baysor"],
                                 file("https://raw.githubusercontent.com/khersameesh24/test-datasets/baysor/transcripts.parquet", checkIfExists: true),
                                 file("https://raw.githubusercontent.com/khersameesh24/test-datasets/baysor/config/xenium.toml", checkIfExists: true)
@@ -41,7 +41,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.of([
+                input[0] = channel.of([
                                 [id: "test_run_baysor"],
                                 file("https://raw.githubusercontent.com/khersameesh24/test-datasets/baysor/transcripts.parquet", checkIfExists: true),
                                 file("https://raw.githubusercontent.com/khersameesh24/test-datasets/baysor/config/xenium.toml", checkIfExists: true)

diff --git a/modules/local/baysor/run/tests/main.nf.test b/modules/local/baysor/run/tests/main.nf.test
@@ -16,7 +16,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.of([
+                input[0] = channel.of([
                                 [id: "test_run_baysor"],
                                 file("https://raw.githubusercontent.com/khersameesh24/test-datasets/baysor/transcripts.parquet", checkIfExists: true),
                                 [],
@@ -46,7 +46,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.of([
+                input[0] = channel.of([
                                 [id: "test_run_baysor"],
                                 file("https://raw.githubusercontent.com/khersameesh24/test-datasets/baysor/transcripts.parquet", checkIfExists: true),
                                 [],

diff --git a/modules/local/baysor/segfree/tests/main.nf.test b/modules/local/baysor/segfree/tests/main.nf.test
@@ -15,7 +15,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.of([
+                input[0] = channel.of([
                                 [id: "test_run_baysor"],
                                 file("https://raw.githubusercontent.com/khersameesh24/test-datasets/baysor/transcripts.parquet", checkIfExists: true),
                                 file("https://raw.githubusercontent.com/khersameesh24/test-datasets/baysor/config/xenium.toml", checkIfExists: true)
@@ -41,7 +41,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.of([
+                input[0] = channel.of([
                                 [id: "test_run_baysor"],
                                 file("https://raw.githubusercontent.com/khersameesh24/test-datasets/baysor/transcripts.parquet", checkIfExists: true),
                                 file("https://raw.githubusercontent.com/khersameesh24/test-datasets/baysor/config/xenium.toml", checkIfExists: true)

diff --git a/modules/local/ficture/model/main.nf b/modules/local/ficture/model/main.nf
@@ -20,7 +20,6 @@ process FICTURE {
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
     def features_list = features ? "--in-feature ${features}": ""
 
     """
@@ -33,12 +32,11 @@ process FICTURE {
         --n-factor 6,12 \\
         --n-jobs ${task.cpus} \\
         --plot-each-factor \\
-        --all
+        --all \\
+        ${args}
     """
 
     stub:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
     """
     mkdir -p results/
     """

diff --git a/modules/local/ficture/preprocess/main.nf b/modules/local/ficture/preprocess/main.nf
@@ -27,7 +27,8 @@ process FICTURE_PREPROCESS {
     ficture_preprocess.py \\
         --transcripts ${transcripts} \\
         ${features_arg} \\
-        --negative-control-regex '${params.negative_control_regex}'
+        --negative-control-regex '${params.negative_control_regex}' \\
+        ${args}
     """
 
     stub:

diff --git a/modules/local/proseg/proseg2baysor/tests/main.nf.test b/modules/local/proseg/proseg2baysor/tests/main.nf.test
@@ -30,7 +30,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.of([
+                input[0] = channel.of([
                             [id: "test_run_proseg2baysor"],
                         ]).combine(PROSEG.out.seg_outs, by: 0)
                 """
@@ -53,7 +53,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.of([
+                input[0] = channel.of([
                             [id: "test_run_proseg2baysor"],
                         ]).combine(PROSEG.out.seg_outs, by: 0)
                 """

diff --git a/modules/local/resolift/tests/tags.yml b/modules/local/resolift/tests/tags.yml
diff --git a/modules/local/utility/convert_mask_uint32/main.nf b/modules/local/utility/convert_mask_uint32/main.nf
@@ -16,7 +16,6 @@ process CONVERT_MASK_UINT32 {
     tag "${meta.id}"
     label 'process_low'
 
-    conda "conda-forge::python=3.12 conda-forge::tifffile conda-forge::numpy"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/d9/d964e0bef867bb2ff1a309c9c087d8d83ac734ce3aa315dd8311d4c1bfdafd8e/data' :
         'community.wave.seqera.io/library/python_pip_imagecodecs_nvidia-cublas-cu12_pruned:b668bcb6d531d350' }"

diff --git a/modules/local/utility/extract_dapi/main.nf b/modules/local/utility/extract_dapi/main.nf
@@ -16,7 +16,6 @@ process EXTRACT_DAPI {
     tag "${meta.id}"
     label 'process_low'
 
-    conda "conda-forge::python=3.12 conda-forge::tifffile conda-forge::numpy"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/d9/d964e0bef867bb2ff1a309c9c087d8d83ac734ce3aa315dd8311d4c1bfdafd8e/data' :
         'community.wave.seqera.io/library/python_pip_imagecodecs_nvidia-cublas-cu12_pruned:b668bcb6d531d350' }"

diff --git a/...y/spatialconverter/parquet_to_csv/main.nf → modules/local/utility/parquet_to_csv/main.nf b/...y/spatialconverter/parquet_to_csv/main.nf → modules/local/utility/parquet_to_csv/main.nf
diff --git a/.../spatialconverter/parquet_to_csv/meta.yml → ...les/local/utility/parquet_to_csv/meta.yml b/.../spatialconverter/parquet_to_csv/meta.yml → ...les/local/utility/parquet_to_csv/meta.yml
@@ -1,9 +1,9 @@
-name: "spatialconverter_parquet_to_csv"
+name: "parquet_to_csv"
 description: Tool suite for spatial omics data conversions.
 keywords:
   - xenium
 tools:
-  - "spatialconverter":
+  - "parquet_to_csv":
       description: "Collects functions to convert data formats for various types of data processing and analysis for spatial omics data."
       homepage: "https://github.com/heylf/spatialconverter"
       documentation: "https://github.com/heylf/spatialconverter"

diff --git a/...o_csv/resources/usr/bin/parquet_to_csv.py → ...o_csv/resources/usr/bin/parquet_to_csv.py b/...o_csv/resources/usr/bin/parquet_to_csv.py → ...o_csv/resources/usr/bin/parquet_to_csv.py
diff --git a/modules/nf-core/xeniumranger/import-segmentation/tests/main.nf.test b/modules/nf-core/xeniumranger/import-segmentation/tests/main.nf.test
diff --git a/modules/nf-core/xeniumranger/relabel/tests/main.nf.test b/modules/nf-core/xeniumranger/relabel/tests/main.nf.test
diff --git a/modules/nf-core/xeniumranger/resegment/tests/main.nf.test b/modules/nf-core/xeniumranger/resegment/tests/main.nf.test
diff --git a/nextflow.config b/nextflow.config
@@ -130,7 +130,6 @@ params {
     restrict_concurrency       = false       // restrict running certain process in parallel
 
     // Boilerplate options
-    outdir                       = null
     publish_dir_mode             = 'copy'
     email                        = null
     email_on_fail                = null