Build branch openpipeline_spatial/niche-compass with version niche-compass to openpipeline_spatial on branch niche-compass (86d15c1)

Build pipeline: openpipelines-bio.openpipeline-spatial.niche-compass-lff78

Source commit: 86d15c1b0d

Source message: typo

CHANGELOG.md

@@ -4,7 +4,7 @@
 
 * Bump squidpy to 1.8.1 and spatialdata to 0.7.2 (PR #41).
 
-* Update openpipeline dependencies to v4.0.1 (PR #42).
+* Update openpipeline dependencies to v4.0.2 (PR #42).
 
 # openpipeline_spatial 0.2.0
 

_viash.yaml

@@ -10,7 +10,7 @@ repositories:
   - name: openpipeline
     repo: openpipeline
     type: vsh
-    tag: v4.0.1
+    tag: v4.0.2
 info:
   test_resources:
     - type: s3

src/workflows/niche/nichecompass_leiden/main.nf

@@ -28,7 +28,12 @@ workflow run_wf {
     
     | flatMap {id, state ->
       def outputDir = state.output
-      def files = readCsv(state.output_files.toUriString())
+
+      def csv = state.output_files.splitCsv(strip: true, sep: ",").findAll{!it[0].startsWith("#")}
+      def header = csv.head()
+      def files = csv.tail().collect { row ->
+          [header, row].transpose().collectEntries()
+      }
       
       files.collect{ dat ->
         def new_id = dat.name // unique sample ids

target/_private/executable/filter/subset_cosmx/.config.vsh.yaml

@@ -112,7 +112,7 @@ repositories:
 - type: "vsh"
   name: "openpipeline"
   repo: "openpipeline"
-  tag: "v4.0.1"
+  tag: "v4.0.2"
 links:
   repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
   docker_registry: "ghcr.io"
@@ -227,7 +227,7 @@ build_info:
   output: "target/_private/executable/filter/subset_cosmx"
   executable: "target/_private/executable/filter/subset_cosmx/subset_cosmx"
   viash_version: "0.9.4"
-  git_commit: "1d17a50229be6fb6702bda689aada82de1c9c56c"
+  git_commit: "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
@@ -241,7 +241,7 @@ package_config:
   - type: "vsh"
     name: "openpipeline"
     repo: "openpipeline"
-    tag: "v4.0.1"
+    tag: "v4.0.2"
   viash_version: "0.9.4"
   source: "src"
   target: "target"

target/_private/executable/filter/subset_cosmx/subset_cosmx

@@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dorien Roosen, Weiwei Schultz"
 LABEL org.opencontainers.image.description="Companion container for running component filter subset_cosmx"
-LABEL org.opencontainers.image.created="2026-02-16T10:14:22Z"
+LABEL org.opencontainers.image.created="2026-02-16T13:09:08Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="1d17a50229be6fb6702bda689aada82de1c9c56c"
+LABEL org.opencontainers.image.revision="86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc"
 LABEL org.opencontainers.image.version="niche-compass"
 
 VIASHDOCKER

target/_private/nextflow/filter/subset_cosmx/.config.vsh.yaml

@@ -112,7 +112,7 @@ repositories:
 - type: "vsh"
   name: "openpipeline"
   repo: "openpipeline"
-  tag: "v4.0.1"
+  tag: "v4.0.2"
 links:
   repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
   docker_registry: "ghcr.io"
@@ -227,7 +227,7 @@ build_info:
   output: "target/_private/nextflow/filter/subset_cosmx"
   executable: "target/_private/nextflow/filter/subset_cosmx/main.nf"
   viash_version: "0.9.4"
-  git_commit: "1d17a50229be6fb6702bda689aada82de1c9c56c"
+  git_commit: "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
@@ -241,7 +241,7 @@ package_config:
   - type: "vsh"
     name: "openpipeline"
     repo: "openpipeline"
-    tag: "v4.0.1"
+    tag: "v4.0.2"
   viash_version: "0.9.4"
   source: "src"
   target: "target"

target/_private/nextflow/filter/subset_cosmx/main.nf

@@ -3187,7 +3187,7 @@ meta = [
       "type" : "vsh",
       "name" : "openpipeline",
       "repo" : "openpipeline",
-      "tag" : "v4.0.1"
+      "tag" : "v4.0.2"
     }
   ],
   "links" : {
@@ -3333,7 +3333,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/_private/nextflow/filter/subset_cosmx",
     "viash_version" : "0.9.4",
-    "git_commit" : "1d17a50229be6fb6702bda689aada82de1c9c56c",
+    "git_commit" : "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
   },
   "package_config" : {
@@ -3353,7 +3353,7 @@ meta = [
         "type" : "vsh",
         "name" : "openpipeline",
         "repo" : "openpipeline",
-        "tag" : "v4.0.1"
+        "tag" : "v4.0.2"
       }
     ],
     "viash_version" : "0.9.4",

target/_test/executable/test_workflows/ingestion/spaceranger_mapping_test/.config.vsh.yaml

@@ -48,7 +48,7 @@ repositories:
 - type: "vsh"
   name: "openpipeline"
   repo: "openpipeline"
-  tag: "v4.0.1"
+  tag: "v4.0.2"
 links:
   repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
   docker_registry: "ghcr.io"
@@ -157,7 +157,7 @@ build_info:
   output: "target/_test/executable/test_workflows/ingestion/spaceranger_mapping_test"
   executable: "target/_test/executable/test_workflows/ingestion/spaceranger_mapping_test/spaceranger_mapping_test"
   viash_version: "0.9.4"
-  git_commit: "1d17a50229be6fb6702bda689aada82de1c9c56c"
+  git_commit: "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
@@ -171,7 +171,7 @@ package_config:
   - type: "vsh"
     name: "openpipeline"
     repo: "openpipeline"
-    tag: "v4.0.1"
+    tag: "v4.0.2"
   viash_version: "0.9.4"
   source: "src"
   target: "target"

target/_test/executable/test_workflows/ingestion/spaceranger_mapping_test/spaceranger_mapping_test

@@ -459,9 +459,9 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component test_workflows/ingestion spaceranger_mapping_test"
-LABEL org.opencontainers.image.created="2026-02-16T10:14:21Z"
+LABEL org.opencontainers.image.created="2026-02-16T13:09:07Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="1d17a50229be6fb6702bda689aada82de1c9c56c"
+LABEL org.opencontainers.image.revision="86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc"
 LABEL org.opencontainers.image.version="niche-compass"
 
 VIASHDOCKER

target/_test/executable/test_workflows/niche/nichecompass_leiden_test/.config.vsh.yaml

@@ -47,7 +47,7 @@ repositories:
 - type: "vsh"
   name: "openpipeline"
   repo: "openpipeline"
-  tag: "v4.0.1"
+  tag: "v4.0.2"
 links:
   repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
   docker_registry: "ghcr.io"
@@ -156,7 +156,7 @@ build_info:
   output: "target/_test/executable/test_workflows/niche/nichecompass_leiden_test"
   executable: "target/_test/executable/test_workflows/niche/nichecompass_leiden_test/nichecompass_leiden_test"
   viash_version: "0.9.4"
-  git_commit: "1d17a50229be6fb6702bda689aada82de1c9c56c"
+  git_commit: "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
@@ -170,7 +170,7 @@ package_config:
   - type: "vsh"
     name: "openpipeline"
     repo: "openpipeline"
-    tag: "v4.0.1"
+    tag: "v4.0.2"
   viash_version: "0.9.4"
   source: "src"
   target: "target"

target/_test/executable/test_workflows/niche/nichecompass_leiden_test/nichecompass_leiden_test

@@ -459,9 +459,9 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component test_workflows/niche nichecompass_leiden_test"
-LABEL org.opencontainers.image.created="2026-02-16T10:14:21Z"
+LABEL org.opencontainers.image.created="2026-02-16T13:09:07Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="1d17a50229be6fb6702bda689aada82de1c9c56c"
+LABEL org.opencontainers.image.revision="86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc"
 LABEL org.opencontainers.image.version="niche-compass"
 
 VIASHDOCKER

target/_test/nextflow/test_workflows/ingestion/spaceranger_mapping_test/.config.vsh.yaml

@@ -48,7 +48,7 @@ repositories:
 - type: "vsh"
   name: "openpipeline"
   repo: "openpipeline"
-  tag: "v4.0.1"
+  tag: "v4.0.2"
 links:
   repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
   docker_registry: "ghcr.io"
@@ -157,7 +157,7 @@ build_info:
   output: "target/_test/nextflow/test_workflows/ingestion/spaceranger_mapping_test"
   executable: "target/_test/nextflow/test_workflows/ingestion/spaceranger_mapping_test/main.nf"
   viash_version: "0.9.4"
-  git_commit: "1d17a50229be6fb6702bda689aada82de1c9c56c"
+  git_commit: "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
@@ -171,7 +171,7 @@ package_config:
   - type: "vsh"
     name: "openpipeline"
     repo: "openpipeline"
-    tag: "v4.0.1"
+    tag: "v4.0.2"
   viash_version: "0.9.4"
   source: "src"
   target: "target"

target/_test/nextflow/test_workflows/ingestion/spaceranger_mapping_test/main.nf

@@ -3104,7 +3104,7 @@ meta = [
       "type" : "vsh",
       "name" : "openpipeline",
       "repo" : "openpipeline",
-      "tag" : "v4.0.1"
+      "tag" : "v4.0.2"
     }
   ],
   "links" : {
@@ -3235,7 +3235,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/_test/nextflow/test_workflows/ingestion/spaceranger_mapping_test",
     "viash_version" : "0.9.4",
-    "git_commit" : "1d17a50229be6fb6702bda689aada82de1c9c56c",
+    "git_commit" : "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
   },
   "package_config" : {
@@ -3255,7 +3255,7 @@ meta = [
         "type" : "vsh",
         "name" : "openpipeline",
         "repo" : "openpipeline",
-        "tag" : "v4.0.1"
+        "tag" : "v4.0.2"
       }
     ],
     "viash_version" : "0.9.4",

target/_test/nextflow/test_workflows/niche/nichecompass_leiden_test/.config.vsh.yaml

@@ -47,7 +47,7 @@ repositories:
 - type: "vsh"
   name: "openpipeline"
   repo: "openpipeline"
-  tag: "v4.0.1"
+  tag: "v4.0.2"
 links:
   repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
   docker_registry: "ghcr.io"
@@ -156,7 +156,7 @@ build_info:
   output: "target/_test/nextflow/test_workflows/niche/nichecompass_leiden_test"
   executable: "target/_test/nextflow/test_workflows/niche/nichecompass_leiden_test/main.nf"
   viash_version: "0.9.4"
-  git_commit: "1d17a50229be6fb6702bda689aada82de1c9c56c"
+  git_commit: "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
@@ -170,7 +170,7 @@ package_config:
   - type: "vsh"
     name: "openpipeline"
     repo: "openpipeline"
-    tag: "v4.0.1"
+    tag: "v4.0.2"
   viash_version: "0.9.4"
   source: "src"
   target: "target"

target/_test/nextflow/test_workflows/niche/nichecompass_leiden_test/main.nf

@@ -3104,7 +3104,7 @@ meta = [
       "type" : "vsh",
       "name" : "openpipeline",
       "repo" : "openpipeline",
-      "tag" : "v4.0.1"
+      "tag" : "v4.0.2"
     }
   ],
   "links" : {
@@ -3235,7 +3235,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/_test/nextflow/test_workflows/niche/nichecompass_leiden_test",
     "viash_version" : "0.9.4",
-    "git_commit" : "1d17a50229be6fb6702bda689aada82de1c9c56c",
+    "git_commit" : "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
   },
   "package_config" : {
@@ -3255,7 +3255,7 @@ meta = [
         "type" : "vsh",
         "name" : "openpipeline",
         "repo" : "openpipeline",
-        "tag" : "v4.0.1"
+        "tag" : "v4.0.2"
       }
     ],
     "viash_version" : "0.9.4",

target/dependencies/vsh/vsh/openpipeline/v4.0.2/_private/nextflow/workflows/multiomics/split_modalities/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "split_modalities"
 namespace: "workflows/multiomics"
-version: "v4.0.1"
+version: "v4.0.2"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -183,13 +183,13 @@ build_info:
   output: "target/_private/nextflow/workflows/multiomics/split_modalities"
   executable: "target/_private/nextflow/workflows/multiomics/split_modalities/main.nf"
   viash_version: "0.9.4"
-  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
+  git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
   dependencies:
   - "target/nextflow/dataflow/split_modalities"
 package_config:
   name: "openpipeline"
-  version: "v4.0.1"
+  version: "v4.0.2"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -219,7 +219,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.2'"
   keywords:
   - "single-cell"
   - "multimodal"

target/dependencies/vsh/vsh/openpipeline/v4.0.2/_private/nextflow/workflows/multiomics/split_modalities/main.nf

@@ -1,4 +1,4 @@
-// split_modalities v4.0.1
+// split_modalities v4.0.2
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "split_modalities",
   "namespace" : "workflows/multiomics",
-  "version" : "v4.0.1",
+  "version" : "v4.0.2",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3274,12 +3274,12 @@ meta = [
     "engine" : "native",
     "output" : "/workdir/root/repo/target/_private/nextflow/workflows/multiomics/split_modalities",
     "viash_version" : "0.9.4",
-    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
+    "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.1",
+    "version" : "v4.0.2",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3304,7 +3304,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.2'"
     ],
     "keywords" : [
       "single-cell",

target/dependencies/vsh/vsh/openpipeline/v4.0.2/_private/nextflow/workflows/multiomics/split_modalities/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'workflows/multiomics/split_modalities'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.1'
+  version = 'v4.0.2'
   description = 'A pipeline to split a multimodal mudata files into several unimodal mudata files.'
   author = 'Dries Schaumont'
 }

target/dependencies/vsh/vsh/openpipeline/v4.0.2/_private/nextflow/workflows/rna/log_normalize/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "log_normalize"
 namespace: "workflows/rna"
-version: "v4.0.1"
+version: "v4.0.2"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -198,7 +198,7 @@ build_info:
   output: "target/_private/nextflow/workflows/rna/log_normalize"
   executable: "target/_private/nextflow/workflows/rna/log_normalize/main.nf"
   viash_version: "0.9.4"
-  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
+  git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
   dependencies:
   - "target/nextflow/transform/normalize_total"
@@ -206,7 +206,7 @@ build_info:
   - "target/nextflow/transform/delete_layer"
 package_config:
   name: "openpipeline"
-  version: "v4.0.1"
+  version: "v4.0.2"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -236,7 +236,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.2'"
   keywords:
   - "single-cell"
   - "multimodal"

target/dependencies/vsh/vsh/openpipeline/v4.0.2/_private/nextflow/workflows/rna/log_normalize/main.nf

@@ -1,4 +1,4 @@
-// log_normalize v4.0.1
+// log_normalize v4.0.2
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "log_normalize",
   "namespace" : "workflows/rna",
-  "version" : "v4.0.1",
+  "version" : "v4.0.2",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3294,12 +3294,12 @@ meta = [
     "engine" : "native",
     "output" : "/workdir/root/repo/target/_private/nextflow/workflows/rna/log_normalize",
     "viash_version" : "0.9.4",
-    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
+    "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.1",
+    "version" : "v4.0.2",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3324,7 +3324,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.2'"
     ],
     "keywords" : [
       "single-cell",

target/dependencies/vsh/vsh/openpipeline/v4.0.2/_private/nextflow/workflows/rna/log_normalize/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'workflows/rna/log_normalize'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.1'
+  version = 'v4.0.2'
   description = 'Performs normalization and subsequent log-transformation of raw count data.'
   author = 'Dries Schaumont'
 }

target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/cluster/leiden/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "leiden"
 namespace: "cluster"
-version: "v4.0.1"
+version: "v4.0.2"
 authors:
 - name: "Dries De Maeyer"
   roles:
@@ -215,7 +215,7 @@ engines:
   id: "docker"
   image: "python:3.13-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.1"
+  target_tag: "v4.0.2"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -258,11 +258,11 @@ build_info:
   output: "target/nextflow/cluster/leiden"
   executable: "target/nextflow/cluster/leiden/main.nf"
   viash_version: "0.9.4"
-  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
+  git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.1"
+  version: "v4.0.2"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -292,7 +292,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.2'"
   keywords:
   - "single-cell"
   - "multimodal"

target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/cluster/leiden/main.nf

@@ -1,4 +1,4 @@
-// leiden v4.0.1
+// leiden v4.0.2
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "leiden",
   "namespace" : "cluster",
-  "version" : "v4.0.1",
+  "version" : "v4.0.2",
   "authors" : [
     {
       "name" : "Dries De Maeyer",
@@ -3294,7 +3294,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.13-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.1",
+      "target_tag" : "v4.0.2",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3352,12 +3352,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/cluster/leiden",
     "viash_version" : "0.9.4",
-    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
+    "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.1",
+    "version" : "v4.0.2",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3382,7 +3382,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.2'"
     ],
     "keywords" : [
       "single-cell",
@@ -4147,7 +4147,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/cluster/leiden",
-    "tag" : "v4.0.1"
+    "tag" : "v4.0.2"
   },
   "label" : [
     "highcpu",

target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/cluster/leiden/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'cluster/leiden'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.1'
+  version = 'v4.0.2'
   description = 'Cluster cells using the [Leiden algorithm] [Traag18] implemented in the [Scanpy framework] [Wolf18]. \nLeiden is an improved version of the [Louvain algorithm] [Blondel08]. \nIt has been proposed for single-cell analysis by [Levine15] [Levine15]. \nThis requires having ran `neighbors/find_neighbors` or `neighbors/bbknn` first.\n\n[Blondel08]: Blondel et al. (2008), Fast unfolding of communities in large networks, J. Stat. Mech.  \n[Levine15]: Levine et al. (2015), Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis, Cell.  \n[Traag18]: Traag et al. (2018), From Louvain to Leiden: guaranteeing well-connected communities arXiv.  \n[Wolf18]: Wolf et al. (2018), Scanpy: large-scale single-cell gene expression data analysis, Genome Biology.  \n'
   author = 'Dries De Maeyer'
 }

target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/concatenate_h5mu/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "concatenate_h5mu"
 namespace: "dataflow"
-version: "v4.0.1"
+version: "v4.0.2"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -253,7 +253,7 @@ engines:
   id: "docker"
   image: "python:3.13-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.1"
+  target_tag: "v4.0.2"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -300,11 +300,11 @@ build_info:
   output: "target/nextflow/dataflow/concatenate_h5mu"
   executable: "target/nextflow/dataflow/concatenate_h5mu/main.nf"
   viash_version: "0.9.4"
-  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
+  git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.1"
+  version: "v4.0.2"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -334,7 +334,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.2'"
   keywords:
   - "single-cell"
   - "multimodal"

target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/concatenate_h5mu/main.nf

@@ -1,4 +1,4 @@
-// concatenate_h5mu v4.0.1
+// concatenate_h5mu v4.0.2
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "concatenate_h5mu",
   "namespace" : "dataflow",
-  "version" : "v4.0.1",
+  "version" : "v4.0.2",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3328,7 +3328,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.13-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.1",
+      "target_tag" : "v4.0.2",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3393,12 +3393,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/dataflow/concatenate_h5mu",
     "viash_version" : "0.9.4",
-    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
+    "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.1",
+    "version" : "v4.0.2",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3423,7 +3423,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.2'"
     ],
     "keywords" : [
       "single-cell",
@@ -4266,7 +4266,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/dataflow/concatenate_h5mu",
-    "tag" : "v4.0.1"
+    "tag" : "v4.0.2"
   },
   "label" : [
     "midcpu",

target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/concatenate_h5mu/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'dataflow/concatenate_h5mu'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.1'
+  version = 'v4.0.2'
   description = 'Concatenate observations from samples in several (uni- and/or multi-modal) MuData files into a single file.\n'
   author = 'Dries Schaumont'
 }

target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/merge/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "merge"
 namespace: "dataflow"
-version: "v4.0.1"
+version: "v4.0.2"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -163,7 +163,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.1"
+  target_tag: "v4.0.2"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -204,11 +204,11 @@ build_info:
   output: "target/nextflow/dataflow/merge"
   executable: "target/nextflow/dataflow/merge/main.nf"
   viash_version: "0.9.4"
-  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
+  git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.1"
+  version: "v4.0.2"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -238,7 +238,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.2'"
   keywords:
   - "single-cell"
   - "multimodal"

target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/merge/main.nf

@@ -1,4 +1,4 @@
-// merge v4.0.1
+// merge v4.0.2
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "merge",
   "namespace" : "dataflow",
-  "version" : "v4.0.1",
+  "version" : "v4.0.2",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3246,7 +3246,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.1",
+      "target_tag" : "v4.0.2",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3302,12 +3302,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/dataflow/merge",
     "viash_version" : "0.9.4",
-    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
+    "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.1",
+    "version" : "v4.0.2",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3332,7 +3332,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.2'"
     ],
     "keywords" : [
       "single-cell",
@@ -3847,7 +3847,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/dataflow/merge",
-    "tag" : "v4.0.1"
+    "tag" : "v4.0.2"
   },
   "label" : [
     "singlecpu",

target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/merge/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'dataflow/merge'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.1'
+  version = 'v4.0.2'
   description = 'Combine one or more single-modality .h5mu files together into one .h5mu file.\n'
   author = 'Dries Schaumont'
 }

target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/split_h5mu/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "split_h5mu"
 namespace: "dataflow"
-version: "v4.0.1"
+version: "v4.0.2"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -203,7 +203,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.1"
+  target_tag: "v4.0.2"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -244,11 +244,11 @@ build_info:
   output: "target/nextflow/dataflow/split_h5mu"
   executable: "target/nextflow/dataflow/split_h5mu/main.nf"
   viash_version: "0.9.4"
-  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
+  git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.1"
+  version: "v4.0.2"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -278,7 +278,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.2'"
   keywords:
   - "single-cell"
   - "multimodal"

target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/split_h5mu/main.nf

@@ -1,4 +1,4 @@
-// split_h5mu v4.0.1
+// split_h5mu v4.0.2
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "split_h5mu",
   "namespace" : "dataflow",
-  "version" : "v4.0.1",
+  "version" : "v4.0.2",
   "authors" : [
     {
       "name" : "Dorien Roosen",
@@ -3285,7 +3285,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.1",
+      "target_tag" : "v4.0.2",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3341,12 +3341,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/dataflow/split_h5mu",
     "viash_version" : "0.9.4",
-    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
+    "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.1",
+    "version" : "v4.0.2",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3371,7 +3371,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.2'"
     ],
     "keywords" : [
       "single-cell",
@@ -3908,7 +3908,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/dataflow/split_h5mu",
-    "tag" : "v4.0.1"
+    "tag" : "v4.0.2"
   },
   "label" : [
     "lowcpu",

target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/split_h5mu/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'dataflow/split_h5mu'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.1'
+  version = 'v4.0.2'
   description = 'Split the samples of a single modality from a .h5mu (multimodal) sample into seperate .h5mu files based on the values of an .obs column of this modality. \n'
   author = 'Dorien Roosen'
 }

target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/split_modalities/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "split_modalities"
 namespace: "dataflow"
-version: "v4.0.1"
+version: "v4.0.2"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -190,7 +190,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.1"
+  target_tag: "v4.0.2"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -231,11 +231,11 @@ build_info:
   output: "target/nextflow/dataflow/split_modalities"
   executable: "target/nextflow/dataflow/split_modalities/main.nf"
   viash_version: "0.9.4"
-  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
+  git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.1"
+  version: "v4.0.2"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -265,7 +265,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.2'"
   keywords:
   - "single-cell"
   - "multimodal"

target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/split_modalities/main.nf

@@ -1,4 +1,4 @@
-// split_modalities v4.0.1
+// split_modalities v4.0.2
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "split_modalities",
   "namespace" : "dataflow",
-  "version" : "v4.0.1",
+  "version" : "v4.0.2",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3280,7 +3280,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.1",
+      "target_tag" : "v4.0.2",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3336,12 +3336,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/dataflow/split_modalities",
     "viash_version" : "0.9.4",
-    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
+    "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.1",
+    "version" : "v4.0.2",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3366,7 +3366,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.2'"
     ],
     "keywords" : [
       "single-cell",
@@ -3865,7 +3865,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/dataflow/split_modalities",
-    "tag" : "v4.0.1"
+    "tag" : "v4.0.2"
   },
   "label" : [
     "singlecpu",

target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/split_modalities/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'dataflow/split_modalities'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.1'
+  version = 'v4.0.2'
   description = 'Split the modalities from a single .h5mu multimodal sample into seperate .h5mu files. \n'
   author = 'Dries Schaumont, Robrecht Cannoodt'
 }

target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dimred/pca/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "pca"
 namespace: "dimred"
-version: "v4.0.1"
+version: "v4.0.2"
 authors:
 - name: "Dries De Maeyer"
   roles:
@@ -240,7 +240,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.1"
+  target_tag: "v4.0.2"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -276,11 +276,11 @@ build_info:
   output: "target/nextflow/dimred/pca"
   executable: "target/nextflow/dimred/pca/main.nf"
   viash_version: "0.9.4"
-  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
+  git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.1"
+  version: "v4.0.2"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -310,7 +310,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.2'"
   keywords:
   - "single-cell"
   - "multimodal"

target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dimred/pca/main.nf

@@ -1,4 +1,4 @@
-// pca v4.0.1
+// pca v4.0.2
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "pca",
   "namespace" : "dimred",
-  "version" : "v4.0.1",
+  "version" : "v4.0.2",
   "authors" : [
     {
       "name" : "Dries De Maeyer",
@@ -3333,7 +3333,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.1",
+      "target_tag" : "v4.0.2",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3380,12 +3380,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/dimred/pca",
     "viash_version" : "0.9.4",
-    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
+    "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.1",
+    "version" : "v4.0.2",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3410,7 +3410,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.2'"
     ],
     "keywords" : [
       "single-cell",
@@ -3933,7 +3933,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/dimred/pca",
-    "tag" : "v4.0.1"
+    "tag" : "v4.0.2"
   },
   "label" : [
     "highcpu",

target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dimred/pca/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'dimred/pca'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.1'
+  version = 'v4.0.2'
   description = 'Computes PCA coordinates, loadings and variance decomposition. Uses the implementation of scikit-learn [Pedregosa11].\n'
   author = 'Dries De Maeyer'
 }

target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dimred/umap/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "umap"
 namespace: "dimred"
-version: "v4.0.1"
+version: "v4.0.2"
 authors:
 - name: "Dries De Maeyer"
   roles:
@@ -294,7 +294,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.1"
+  target_tag: "v4.0.2"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -330,11 +330,11 @@ build_info:
   output: "target/nextflow/dimred/umap"
   executable: "target/nextflow/dimred/umap/main.nf"
   viash_version: "0.9.4"
-  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
+  git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.1"
+  version: "v4.0.2"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -364,7 +364,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.2'"
   keywords:
   - "single-cell"
   - "multimodal"

target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dimred/umap/main.nf

@@ -1,4 +1,4 @@
-// umap v4.0.1
+// umap v4.0.2
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "umap",
   "namespace" : "dimred",
-  "version" : "v4.0.1",
+  "version" : "v4.0.2",
   "authors" : [
     {
       "name" : "Dries De Maeyer",
@@ -3382,7 +3382,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.1",
+      "target_tag" : "v4.0.2",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3429,12 +3429,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/dimred/umap",
     "viash_version" : "0.9.4",
-    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
+    "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.1",
+    "version" : "v4.0.2",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3459,7 +3459,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.2'"
     ],
     "keywords" : [
       "single-cell",
@@ -3971,7 +3971,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/dimred/umap",
-    "tag" : "v4.0.1"
+    "tag" : "v4.0.2"
   },
   "label" : [
     "highcpu",

target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dimred/umap/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'dimred/umap'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.1'
+  version = 'v4.0.2'
   description = 'UMAP (Uniform Manifold Approximation and Projection) is a manifold learning technique suitable for visualizing high-dimensional data. Besides tending to be faster than tSNE, it optimizes the embedding such that it best reflects the topology of the data, which we represent throughout Scanpy using a neighborhood graph. tSNE, by contrast, optimizes the distribution of nearest-neighbor distances in the embedding such that these best match the distribution of distances in the high-dimensional space. We use the implementation of umap-learn [McInnes18]. For a few comparisons of UMAP with tSNE, see this preprint.\n'
   author = 'Dries De Maeyer'
 }

target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/feature_annotation/highly_variable_features_scanpy/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "highly_variable_features_scanpy"
 namespace: "feature_annotation"
-version: "v4.0.1"
+version: "v4.0.2"
 authors:
 - name: "Dries De Maeyer"
   roles:
@@ -342,7 +342,7 @@ engines:
   id: "docker"
   image: "python:3.12"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.1"
+  target_tag: "v4.0.2"
   namespace_separator: "/"
   setup:
   - type: "python"
@@ -381,11 +381,11 @@ build_info:
   output: "target/nextflow/feature_annotation/highly_variable_features_scanpy"
   executable: "target/nextflow/feature_annotation/highly_variable_features_scanpy/main.nf"
   viash_version: "0.9.4"
-  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
+  git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.1"
+  version: "v4.0.2"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -415,7 +415,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.2'"
   keywords:
   - "single-cell"
   - "multimodal"

target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/feature_annotation/highly_variable_features_scanpy/main.nf

@@ -1,4 +1,4 @@
-// highly_variable_features_scanpy v4.0.1
+// highly_variable_features_scanpy v4.0.2
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "highly_variable_features_scanpy",
   "namespace" : "feature_annotation",
-  "version" : "v4.0.1",
+  "version" : "v4.0.2",
   "authors" : [
     {
       "name" : "Dries De Maeyer",
@@ -3430,7 +3430,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.1",
+      "target_tag" : "v4.0.2",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3481,12 +3481,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/feature_annotation/highly_variable_features_scanpy",
     "viash_version" : "0.9.4",
-    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
+    "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.1",
+    "version" : "v4.0.2",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3511,7 +3511,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.2'"
     ],
     "keywords" : [
       "single-cell",
@@ -4110,7 +4110,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/feature_annotation/highly_variable_features_scanpy",
-    "tag" : "v4.0.1"
+    "tag" : "v4.0.2"
   },
   "label" : [
     "singlecpu",

target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/feature_annotation/highly_variable_features_scanpy/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'feature_annotation/highly_variable_features_scanpy'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.1'
+  version = 'v4.0.2'
   description = 'Annotate highly variable features [Satija15] [Zheng17] [Stuart19].\n\nExpects logarithmized data, except when flavor=\'seurat_v3\' in which count data is expected.\n\nDepending on flavor, this reproduces the R-implementations of Seurat [Satija15], Cell Ranger [Zheng17], and Seurat v3 [Stuart19].\n\nFor the dispersion-based methods ([Satija15] and [Zheng17]), the normalized dispersion is obtained by scaling with the mean and standard deviation of the dispersions for features falling into a given bin for mean expression of features. This means that for each bin of mean expression, highly variable features are selected.\n\nFor [Stuart19], a normalized variance for each feature is computed. First, the data are standardized (i.e., z-score normalization per feature) with a regularized standard deviation. Next, the normalized variance is computed as the variance of each feature after the transformation. Features are ranked by the normalized variance.\n'
   author = 'Dries De Maeyer, Robrecht Cannoodt'
 }

target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/delimit_fraction/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "delimit_fraction"
 namespace: "filter"
-version: "v4.0.1"
+version: "v4.0.2"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -219,7 +219,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.1"
+  target_tag: "v4.0.2"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -260,11 +260,11 @@ build_info:
   output: "target/nextflow/filter/delimit_fraction"
   executable: "target/nextflow/filter/delimit_fraction/main.nf"
   viash_version: "0.9.4"
-  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
+  git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.1"
+  version: "v4.0.2"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -294,7 +294,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.2'"
   keywords:
   - "single-cell"
   - "multimodal"

target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/delimit_fraction/main.nf

@@ -1,4 +1,4 @@
-// delimit_fraction v4.0.1
+// delimit_fraction v4.0.2
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "delimit_fraction",
   "namespace" : "filter",
-  "version" : "v4.0.1",
+  "version" : "v4.0.2",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3312,7 +3312,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.1",
+      "target_tag" : "v4.0.2",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3368,12 +3368,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/filter/delimit_fraction",
     "viash_version" : "0.9.4",
-    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
+    "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.1",
+    "version" : "v4.0.2",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3398,7 +3398,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.2'"
     ],
     "keywords" : [
       "single-cell",
@@ -3928,7 +3928,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/filter/delimit_fraction",
-    "tag" : "v4.0.1"
+    "tag" : "v4.0.2"
   },
   "label" : [
     "singlecpu",

target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/delimit_fraction/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'filter/delimit_fraction'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.1'
+  version = 'v4.0.2'
   description = 'Turns a column containing values between 0 and 1 into a boolean column based on thresholds.\n'
   author = 'Dries Schaumont'
 }

target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/do_filter/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "do_filter"
 namespace: "filter"
-version: "v4.0.1"
+version: "v4.0.2"
 authors:
 - name: "Robrecht Cannoodt"
   roles:
@@ -193,7 +193,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.1"
+  target_tag: "v4.0.2"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -228,11 +228,11 @@ build_info:
   output: "target/nextflow/filter/do_filter"
   executable: "target/nextflow/filter/do_filter/main.nf"
   viash_version: "0.9.4"
-  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
+  git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.1"
+  version: "v4.0.2"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -262,7 +262,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.2'"
   keywords:
   - "single-cell"
   - "multimodal"

target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/do_filter/main.nf

@@ -1,4 +1,4 @@
-// do_filter v4.0.1
+// do_filter v4.0.2
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "do_filter",
   "namespace" : "filter",
-  "version" : "v4.0.1",
+  "version" : "v4.0.2",
   "authors" : [
     {
       "name" : "Robrecht Cannoodt",
@@ -3282,7 +3282,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.1",
+      "target_tag" : "v4.0.2",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3328,12 +3328,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/filter/do_filter",
     "viash_version" : "0.9.4",
-    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
+    "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.1",
+    "version" : "v4.0.2",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3358,7 +3358,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.2'"
     ],
     "keywords" : [
       "single-cell",
@@ -3851,7 +3851,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/filter/do_filter",
-    "tag" : "v4.0.1"
+    "tag" : "v4.0.2"
   },
   "label" : [
     "singlecpu",

target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/do_filter/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'filter/do_filter'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.1'
+  version = 'v4.0.2'
   description = 'Remove observations and variables based on specified .obs and .var columns.\n'
   author = 'Robrecht Cannoodt'
 }

target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/filter_with_counts/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "filter_with_counts"
 namespace: "filter"
-version: "v4.0.1"
+version: "v4.0.2"
 authors:
 - name: "Dries De Maeyer"
   roles:
@@ -280,7 +280,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.1"
+  target_tag: "v4.0.2"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -321,11 +321,11 @@ build_info:
   output: "target/nextflow/filter/filter_with_counts"
   executable: "target/nextflow/filter/filter_with_counts/main.nf"
   viash_version: "0.9.4"
-  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
+  git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.1"
+  version: "v4.0.2"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -355,7 +355,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.2'"
   keywords:
   - "single-cell"
   - "multimodal"