5127 new module xenium ranger

.github/workflows/test.yml

@@ -656,6 +656,15 @@ jobs:
             path: subworkflows/nf-core/fastq_align_bwa
           - profile: conda
             path: subworkflows/nf-core/fasta_newick_epang_gappa
+          - profile: conda
+            path: modules/nf-core/xeniumranger/relabel
+          - profile: conda
+            path: modules/nf-core/xeniumranger/rename
+          - profile: conda
+            path: modules/nf-core/xeniumranger/resegment
+          - profile: conda
+            path: modules/nf-core/xeniumranger/import-segmentation
+
     env:
       NXF_ANSI_LOG: false
       NFTEST_VER: "0.9.0"

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: "v3.1.0"
+    rev: "v4.0.0-alpha.8"
     hooks:
       - id: prettier
         additional_dependencies:

modules/nf-core/xeniumranger/Dockerfile

@@ -0,0 +1,29 @@
+#  Use a base image with the required operating system
+FROM ubuntu:20.04 AS builder
+
+LABEL authors="Sameesh Kher <[email protected]>" \
+    description="Docker image containing Xenium Ranger"
+
+RUN apt-get update --allow-releaseinfo-change \
+    && apt-get install -y \
+    && apt-get clean -y && rm -rf /var/lib/apt/lists/*
+
+# copy over xeniumranger
+# the latest version of the xeniumranger tool has been downloaded from https://www.10xgenomics.com/support/software/xenium-ranger/downloads
+COPY xeniumranger-3.0.1.tar.gz /xeniumranger-3.0.1.tar.gz
+
+# install xenium ranger
+RUN tar -xzvf /xeniumranger-3.0.1.tar.gz && \
+    rm /xeniumranger-3.0.1.tar.gz
+
+# Set environment variables
+# ENV PATH="xeniumranger-xenium3.0/bin:$PATH"
+
+# multistage to reduce image size
+FROM ubuntu:20.04
+
+# Set environment variables
+ENV PATH="/xeniumranger-xenium3.0/bin:$PATH"
+
+# copy over xenium from builder
+COPY --from=builder /xeniumranger-xenium3.0 /xeniumranger-xenium3.0/

modules/nf-core/xeniumranger/README.md

@@ -0,0 +1,20 @@
+# Updating the docker container and making a new module release
+
+Xenium Ranger is a commercial tool from 10X Genomics. The container provided for the xeniumranger nf-core module is not provided nor supported by 10x Genomics. Updating the Xenium Ranger versions in the container and pushing the update to Dockerhub needs to be done manually.
+
+1. Navigate to the appropriate download page. - [Xenium Ranger](https://www.10xgenomics.com/support/software/xenium-ranger/downloads): download the tar ball of the desired Xenium Ranger version with `curl` or `wget`. Place this file in the same folder where the Dockerfile lies.
+
+2. Edit the Dockerfile. Update the Xenium Ranger versions in this line:
+   (current version for xenium ranger is fixated at [3.0.1](https://www.10xgenomics.com/support/software/xenium-ranger/downloads) in the dockerfile)
+
+3. Create and test the container:
+
+```bash
+docker build . -t quay.io/nf-core/xeniumranger:<VERSION>
+```
+
+4. Access rights are needed to push the container to the Dockerhub nfcore organization, please ask a core team member to do so.
+
+```bash
+docker push quay.io/nf-core/xeniumranger:<VERSION>
+```

modules/nf-core/xeniumranger/import-segmentation/main.nf

@@ -0,0 +1,82 @@
+process XENIUMRANGER_IMPORT_SEGMENTATION {
+    tag "$meta.id"
+    label 'process_high'
+
+    container "nf-core/xeniumranger:3.0.1"
+
+    input:
+    val(meta)
+    path(xenium_bundle)
+    val(expansion_distance)
+    path(coordinate_transform)
+    path(nuclei)
+    path(cells)
+    path(transcript_assignment)
+    path(viz_polygons)
+
+    output:
+    tuple val(meta), path("**/outs/**"), emit: outs
+    path "versions.yml", emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "XENIUMRANGER_IMPORT-SEGMENTATION module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    // image based segmentation options
+    def expansion_distance = expansion_distance ? "--expansion-distance=\"${expansion_distance}\"": "" // expansion distance (default - 5, range - 0 - 100)
+    def coordinate_transform = coordinate_transform ? "--coordinate-transform=\"${coordinate_transform}\"": ""
+
+    def nuclei_detection = nuclei ? "--nuclei=\"${nuclei}\"": ""
+    def cells = cells ? "--cells=\"${cells}\"": ""
+
+    // transcript based segmentation
+    def transcript_assignment = transcript_assignment ? "--transcript-assignment=\"${transcript_assignment}\"": ""
+    def viz_polygons = viz_polygons ? "--viz-polygons=\"${viz_polygons}\"":""
+
+    // shared argument
+    def units = coordinate_transform ? "--units=microns": "--units=pixels"
+
+    """
+    xeniumranger import-segmentation \\
+        --id="${prefix}" \\
+        --xenium-bundle="${xenium_bundle}" \\
+        --localcores=${task.cpus} \\
+        --localmem=${task.memory.toGiga()} \\
+        ${coordinate_transform} \\
+        ${nuclei_detection} \\
+        ${cells} \\
+        ${expansion_distance} \\
+        ${transcript_assignment} \\
+        ${viz_polygons} \\
+        ${units} \\
+        ${args}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        xeniumranger: \$(xeniumranger -V | sed -e "s/xeniumranger-/- /g")
+    END_VERSIONS
+    """
+
+    stub:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "XENIUMRANGER_IMPORT-SEGMENTATION module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    mkdir -p "${prefix}/outs/"
+    touch "${prefix}/outs/fake_file.txt"
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        xeniumranger: \$(xeniumranger -V | sed -e "s/xeniumranger-/- /g")
+    END_VERSIONS
+    """
+}

modules/nf-core/xeniumranger/import-segmentation/meta.yml

@@ -0,0 +1,84 @@
+name: xeniumranger_import_segmentation
+description: The xeniumranger import-segmentation module allows you to specify 2D
+  nuclei and/or cell segmentation results for assigning transcripts to cells and recalculate
+  all Xenium Onboard Analysis (XOA) outputs that depend on segmentation. Segmentation
+  results can be generated by community-developed tools or prior Xenium segmentation
+  result.
+keywords:
+  - spatial
+  - segmentation
+  - import segmentation
+  - nuclear segmentation
+  - cell segmentation
+  - xeniumranger
+  - imaging
+tools:
+  - xeniumranger:
+      description: |
+        Xenium Ranger is a set of analysis pipelines that process Xenium In Situ Gene Expression data to relabel, resegment, or import new segmentation results from community-developed tools. Xenium Ranger provides flexible off-instrument reanalysis of Xenium In Situ data. Relabel transcripts, resegment cells with the latest 10x segmentation algorithms, or import your own segmentation data to assign transcripts to cells.
+      homepage: "https://www.10xgenomics.com/support/software/xenium-ranger/latest"
+      documentation: "https://www.10xgenomics.com/support/software/xenium-ranger/latest/getting-started"
+      tool_dev_url: "https://www.10xgenomics.com/support/software/xenium-ranger/latest/analysis"
+      licence:
+        - "10x Genomics EULA"
+      identifier: ""
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing run information
+          e.g. [id:'xenium_bundle_path']
+  - - xenium_bundle:
+        type: directory
+        description: Path to the xenium output bundle generated by the Xenium Onboard
+          Analysis pipeline
+  - - expansion_distance:
+        type: integer
+        description: Nuclei boundary expansion distance in µm. Only for use when nucleus
+          segmentation provided as input. Default-5 (accepted range 0 - 100)
+  - - coordinate_transform:
+        type: file
+        description: Image alignment file containing similarity transform matrix e.g.,
+          the _imagealignment.csv file exported from Xenium Explorer
+  - - nuclei:
+        type: file
+        description: |
+          Label mask (TIFF or NPY), polygons of nucleus segmentations (GeoJSON FeatureCollection), or Xenium Onboard Analysis cells.zarr.zip (the nucleus masks as input).
+          --nuclei will use nucleusGeometry polygon if it exists in the GeoJSON (i.e., for QuPath-like GeoJSON files),
+          or geometry if it does not. Error if --transcript-assignment argument is used.
+  - - cells:
+        type: file
+        description: |
+          Label mask (TIFF or NPY), polygons of cell segmentations (GeoJSON FeatureCollection), or Xenium Onboard Analysis cells.zarr.zip (the cell masks as input).
+          Features with a non-cell objectType will be ignored. Error if --transcript-assignment argument is used.
+          In Xenium Ranger v2.0, --nuclei no longer needs to be used with --cells.
+  - - transcript_assignment:
+        type: file
+        description: |
+          Transcript CSV with cell assignment from Baysor v0.6. Error if --cells or --nuclei arguments are used.
+  - - viz_polygons:
+        type: file
+        description: |
+          Cell boundary polygons (GeoJSON) for visualization from Baysor v0.6. Required if --transcript-assignment argument used. Error if --cells or --nuclei arguments used.
+output:
+  - outs:
+      - meta:
+          type: file
+          description: Files containing the outputs of Cell Ranger, see official 10X Genomics
+            documentation for a complete list
+          pattern: "${meta.id}/outs/*"
+      - "**/outs/**":
+          type: file
+          description: Files containing the outputs of xenium ranger, see official 10X
+            Genomics documentation for a complete list of outputs
+          pattern: "${meta.id}/outs/*"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@khersameesh24"
+maintainers:
+  - "@khersameesh24"