Build branch build/main with version build_main (491efce)

Build pipeline: openpipelines-bio.openpipeline-spatial.build-main-kj8js

Source commit: 491efceaaf

Source message: deploy: 7f820d2607f3e1fabc0183915d1bb427715e18ae

CHANGELOG.md

@@ -0,0 +1,5 @@
+# openpipeline_spatial 0.0.0
+
+## NEW FUNCTIONALITY
+
+* `mapping/spaceranger_count`: Added a spaceranger count component (PR #2).

resources_test_scripts/reference_tiny.sh

@@ -0,0 +1,19 @@
+#!/bin/bash
+
+set -eo pipefail
+
+# get the root of the directory
+REPO_ROOT=$(git rev-parse --show-toplevel)
+
+# ensure that the command below is run from the root of the repository
+cd "$REPO_ROOT"
+DIR="resources_test/GRCh38"
+
+mkdir -p $DIR
+
+aws s3 sync \
+    --profile di \
+    s3://openpipelines-bio/openpipeline_spatial/resources_test/GRCh38 \
+    "$DIR" \
+    --delete \
+    --dryrun

resources_test_scripts/visium_tiny.sh

@@ -0,0 +1,35 @@
+#!/bin/bash
+
+set -eo pipefail
+
+# get the root of the directory
+REPO_ROOT=$(git rev-parse --show-toplevel)
+
+# Define absolute directory path
+DIR="$REPO_ROOT/resources_test/visium"
+
+# from https://www.10xgenomics.com/resources/datasets/human-ovarian-cancer-1-standard
+mkdir -p "$DIR"
+
+# Input Files - download to the specific directory
+curl -o "$DIR/Visium_FFPE_Human_Ovarian_Cancer_fastqs.tar" https://cf.10xgenomics.com/samples/spatial-exp/1.3.0/Visium_FFPE_Human_Ovarian_Cancer/Visium_FFPE_Human_Ovarian_Cancer_fastqs.tar
+curl -o "$DIR/Visium_FFPE_Human_Ovarian_Cancer_image.jpg" https://cf.10xgenomics.com/samples/spatial-exp/1.3.0/Visium_FFPE_Human_Ovarian_Cancer/Visium_FFPE_Human_Ovarian_Cancer_image.jpg
+curl -o "$DIR/Visium_FFPE_Human_Ovarian_Cancer_probe_set.csv" https://cf.10xgenomics.com/samples/spatial-exp/1.3.0/Visium_FFPE_Human_Ovarian_Cancer/Visium_FFPE_Human_Ovarian_Cancer_probe_set.csv
+
+# Extract in the specific directory
+tar xvf "$DIR/Visium_FFPE_Human_Ovarian_Cancer_fastqs.tar" -C "$DIR"
+
+# Create subsampled dataset with ImageMagick
+# https://imagemagick.org/index.php
+mkdir -p "$DIR/subsampled"
+convert "$DIR/Visium_FFPE_Human_Ovarian_Cancer_image.jpg" -resize 2000x2000 "$DIR/subsampled/Visium_FFPE_Human_Ovarian_Cancer_image.jpg"
+for f in "$DIR"/Visium_FFPE_Human_Ovarian_Cancer_fastqs/*L001*R*; do 
+  gzip -cdf "$f" | head -n 40000 | gzip -c > "$DIR/subsampled/$(basename "$f")"; 
+done
+
+aws s3 sync \
+    --profile di \
+    "$DIR" \
+    s3://openpipelines-bio/openpipeline_spatial/resources_test/visium \
+    --delete \
+    --dryrun

resources_test_scripts/xenium_tiny.sh

@@ -5,12 +5,10 @@ set -eo pipefail
 # get the root of the directory
 REPO_ROOT=$(git rev-parse --show-toplevel)
 
-# ensure that the command below is run from the root of the repository
+# Define absolute directory paths
-cd "$REPO_ROOT"
+DIR="$REPO_ROOT/resources_test/xenium"
-
-DIR="resources_test/xenium/"
 ID="xenium_tiny"
-OUT="$DIR/$ID/"
+OUT="$DIR/$ID"
 
 # create tempdir
 MY_TEMP="${VIASH_TEMP:-/tmp}"
@@ -29,11 +27,11 @@ if [ ! -d "$OUT" ]; then
     mv "$TMPDIR/xenium_tiny/Xenium_Prime_Mouse_Ileum_tiny_outs/"* "$OUT/"
 fi
 
-viash run src/convert/from_xenium_to_spatialdata/config.vsh.yaml -- \
+viash run "$REPO_ROOT/src/convert/from_xenium_to_spatialdata/config.vsh.yaml" -- \
     --input "$OUT" \
     --output "$DIR/$ID.zarr"
 
-viash run src/convert/from_spatialdata_to_h5mu/config.vsh.yaml -- \
+viash run "$REPO_ROOT/src/convert/from_spatialdata_to_h5mu/config.vsh.yaml" -- \
     --input "$DIR/$ID.zarr" \
     --output "$DIR/$ID.h5mu"
 

src/mapping/spaceranger_count/config.vsh.yaml

@@ -0,0 +1,208 @@
+name: spaceranger_count
+namespace: mapping
+description: Count gene expression and protein expression reads from a single capture area.
+keywords: [spaceranger]
+links:
+  documentation: https://www.10xgenomics.com/support/software/space-ranger/latest/analysis/running-pipelines/space-ranger-count
+authors:
+  - __merge__: /src/authors/jakub_majercik.yaml
+    roles: [ author ]
+argument_groups:
+  - name: Inputs
+    arguments:
+      - type: file
+        name: --gex_reference
+        required: true
+        description: Path of folder containing 10x-compatible reference
+        example: "/path/to/refdata-gex-GRCh38-2020-A"
+
+      - type: file
+        name: --input
+        required: true
+        description: | 
+          Path to a directory containing input FASTQ data. Individual FASTQ files should follow the naming convention of 10x Genomics:
+          [Sample Name]_S[Sample Number]_L[Lane Number]_[Read Type]_001.fastq.gz
+
+          Where:
+          [Sample Name] is the name assigned during sample preparation/sequencing
+          S[Sample Number] is the sample index (usually S1, S2, etc.)
+          L[Lane Number] identifies the sequencing lane (L001, L002, etc.)
+
+          [Read Type] will be one of:
+          R1 - Read 1 (contains the spatial barcode and UMI)
+          R2 - Read 2 (contains the actual cDNA sequence)
+          I1 - Index Read 1 (if applicable)
+          I2 - Index Read 2 (if applicable)
+        example: "/path/to/fastq_folder"
+
+      - type: file
+        name: --probe_set
+        required: true
+        description: CSV file specifying the probe set used
+        example: "Visium_Human_Transcriptome_Probe_Set_v2.0_GRCh38-2020-A.csv"
+
+      - type: file
+        name: --cytaimage
+        required: false
+        description: | 
+          Brightfield image generated by the CytAssist instrument. 
+          When using CytAssist workflow, either this or --image must be provided.
+        example: "cyta_image.tif"
+
+      - type: file
+        name: --image
+        required: false
+        description: | 
+          H&E or fluorescence microscope image in TIFF or JPG format. 
+          Required for standard Visium workflow, optional when using --cytaimage for CytAssist workflow.
+        example: "brightfield.tif"
+
+  - name: Outputs
+    arguments:
+      - type: file
+        name: --output
+        required: true
+        direction: output
+        description: The folder to store the alignment results
+        example: "/path/to/output"
+
+  - name: Slide Information
+    arguments:
+      - type: string
+        name: --slide
+        description: Visium slide serial number (e.g., 'V10J25-015')
+        required: false
+        example: "V10J25-015"
+
+      - type: string
+        name: --area
+        description: Visium capture area identifier (e.g., 'A1')
+        required: false
+        example: "A1"
+
+      - type: string
+        name: --unknown_slide
+        description: | 
+          Use this option if the slide serial number and area were entered incorrectly on the CytAssist 
+          instrument and the correct values are unknown. Not compatible with --slide, --area, or 
+          --slide-file options
+        required: false
+        choices: [visium-1, visium-2, visium-2-large, visium-hd]
+
+      - type: file
+        name: --slidefile
+        description: Slide design file for offline use
+        required: false
+        example: "slide_design.gpr"
+
+      - type: boolean_true
+        name: --override_id
+        description: Overrides the slide serial number and capture area provided in the Cytassist image metadata
+
+  - name: Image Options
+    arguments:
+      - type: file
+        name: --darkimage
+        description: Multi-channel, dark-background fluorescence image
+        required: false
+        example: "fluorescence.tif"
+
+      - type: file
+        name: --colorizedimage
+        description: Color image representing pre-colored dark-background fluorescence images
+        required: false
+        example: "colored_fluorescence.tif"
+
+      - type: integer
+        name: --dapi_index
+        description: Index of DAPI channel (1-indexed) of fluorescence image
+        required: false
+        example: 1
+        min: 1
+
+      - type: double
+        name: --image_scale
+        description: Microns per microscope image pixel
+        required: false
+        example: 0.65
+        min: 0.01
+        max: 10
+
+      - type: boolean
+        name: --reorient_images
+        default: true
+        description: Whether to rotate and mirror image to align fiducial pattern
+
+  - name: Processing Options
+    arguments:
+      - type: boolean
+        name: --create_bam
+        required: true
+        description: Enable or disable BAM file generation
+        default: true
+
+      - type: boolean_true
+        name: --nosecondary
+        description: Disable secondary analysis (e.g., clustering)
+
+      - type: integer
+        name: --r1_length
+        required: false
+        description: Hard trim the input Read 1 to this length before analysis
+        min: 1
+
+      - type: integer
+        name: --r2_length
+        required: false
+        description: Hard trim the input Read 2 to this length before analysis
+        min: 1
+
+      - type: boolean
+        name: --filter_probes
+        default: true
+        description: Whether to filter the probe set using the "included" column
+
+      - type: integer
+        name: --custom_bin_size
+        description: Bin Visium HD data to specified size in microns (4-100, even values only) in addition to the standard binning size (2 µm, 8 µm, 16 µm)
+        min: 4
+        max: 100
+
+  - name: Input Selection
+    arguments:
+      - type: string
+        name: --project
+        required: false
+        description: Project folder name within mkfastq output
+        
+      - type: string
+        name: --sample
+        required: false
+        description: Prefix of FASTQ filenames to select
+
+      - type: integer
+        name: --lanes
+        multiple: true
+        required: false
+        description: Only use FASTQs from selected lanes
+        example: [1,2,3]
+
+resources:
+  - type: bash_script
+    path: script.sh
+test_resources:
+  - type: bash_script
+    path: test.sh
+  - path: /resources_test/visium
+  - path: /resources_test/GRCh38
+engines:
+  - type: docker
+    image: ghcr.io/data-intuitive/spaceranger:3.1
+    setup:
+      - type: docker
+        run: |
+          DEBIAN_FRONTEND=noninteractive apt update && \
+          apt upgrade -y && apt install -y procps && rm -rf /var/lib/apt/lists/*
+runners:
+  - type: executable
+  - type: nextflow

src/mapping/spaceranger_count/script.sh

@@ -0,0 +1,45 @@
+#!/bin/bash
+
+set -eo pipefail
+
+unset_if_false=(
+    par_override_id
+    par_nosecondary
+)
+
+for par in ${unset_if_false[@]}; do
+    test_val="${!par}"
+    [[ "$test_val" == "false" ]] && unset $par
+done
+
+spaceranger count \
+  ${par_output:+--id="$par_output"} \
+  ${par_gex_reference:+--transcriptome="$par_gex_reference"} \
+  ${par_input:+--fastqs="$par_input"} \
+  ${par_probe_set:+--probe-set="$par_probe_set"} \
+  ${par_cytaimage:+--cytaimage="$par_cytaimage"} \
+  ${par_image:+--image="$par_image"} \
+  ${par_slide:+--slide="$par_slide"} \
+  ${par_area:+--area="$par_area"} \
+  ${par_unknown_slide:+--unknown-slide="$par_unknown_slide"} \
+  ${par_slidefile:+--slidefile="$par_slidefile"} \
+  ${par_override_id:+--override-id} \
+  ${par_darkimage:+--darkimage="$par_darkimage"} \
+  ${par_colorizedimage:+--colorizedimage="$par_colorizedimage"} \
+  ${par_dapi_index:+--dapi-index="$par_dapi_index"} \
+  ${par_image_scale:+--image-scale="$par_image_scale"} \
+  ${par_reorient_images:+--reorient-images="$par_reorient_images"} \
+  ${par_create_bam:+--create-bam="$par_create_bam"} \
+  ${par_nosecondary:+--nosecondary} \
+  ${par_r1_length:+--r1-length="$par_r1_length"} \
+  ${par_r2_length:+--r2-length="$par_r2_length"} \
+  ${par_filter_probes:+--filter-probes="$par_filter_probes"} \
+  ${par_custom_bin_size:+--custom-bin-size="$par_custom_bin_size"} \
+  ${par_project:+--project="$par_project"} \
+  ${par_sample:+--sample="$par_sample"} \
+  ${par_lanes:+--lanes="$par_lanes"} \
+  ${meta_cpus:+--localcores="$meta_cpus"} \
+  ${meta_memory_gb:+--localmem=$(($meta_memory_gb-2))}
+
+mv -f "$par_output"/outs/* "$par_output"/
+rm -rf "$par_output"/outs

src/mapping/spaceranger_count/test.sh

@@ -0,0 +1,47 @@
+#!/bin/bash
+
+set -eo pipefail
+
+## VIASH START
+meta_executable="target/native/spaceranger/spaceranger_count/spaceranger_count"
+meta_resources_dir="resources_test"
+## VIASH END
+
+test_data="$meta_resources_dir/visium"
+
+echo "> Default test run"
+"$meta_executable" \
+    --output test_spaceranger \
+    --gex_reference "$meta_resources_dir/GRCh38" \
+    --input "$test_data/subsampled" \
+    --probe_set "$test_data/Visium_FFPE_Human_Ovarian_Cancer_probe_set.csv" \
+    --image "$test_data/subsampled/Visium_FFPE_Human_Ovarian_Cancer_image.jpg" \
+    --unknown_slide visium-1 \
+    --create_bam false
+
+echo "> Checking outputs..."
+
+# Define output directory
+OUT_DIR="test_spaceranger"
+
+# Function to check if file exists and is non-empty
+check_file() {
+    local file=$1
+    local description=$2
+    echo -n "Checking $description... "
+    if [ ! -f "$file" ]; then
+        echo "FAIL (file not found)"
+        exit 1
+    elif [ ! -s "$file" ]; then
+        echo "FAIL (file is empty)"
+        exit 1
+    else
+        echo "OK"
+    fi
+}
+
+# Check essential files
+check_file "$OUT_DIR/web_summary.html" "web summary"
+check_file "$OUT_DIR/metrics_summary.csv" "metrics summary"
+
+echo "> All tests passed successfully!"

target/executable/convert/from_cosmx_to_h5mu/.config.vsh.yaml

@@ -231,7 +231,7 @@ build_info:
   output: "target/executable/convert/from_cosmx_to_h5mu"
   executable: "target/executable/convert/from_cosmx_to_h5mu/from_cosmx_to_h5mu"
   viash_version: "0.9.3"
-  git_commit: "9f2a3e68cb0ae7fc97924d8872376ec7a58afe16"
+  git_commit: "491efceaaf171f50aaa1d28f690c1e974cffc456"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"

target/executable/convert/from_cosmx_to_h5mu/from_cosmx_to_h5mu

@@ -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 convert from_cosmx_to_h5mu"
-LABEL org.opencontainers.image.created="2025-06-11T09:39:26Z"
+LABEL org.opencontainers.image.created="2025-07-10T12:30:15Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="9f2a3e68cb0ae7fc97924d8872376ec7a58afe16"
+LABEL org.opencontainers.image.revision="491efceaaf171f50aaa1d28f690c1e974cffc456"
 LABEL org.opencontainers.image.version="build_main"
 
 VIASHDOCKER

target/executable/convert/from_spatialdata_to_h5mu/.config.vsh.yaml

@@ -217,7 +217,7 @@ build_info:
   output: "target/executable/convert/from_spatialdata_to_h5mu"
   executable: "target/executable/convert/from_spatialdata_to_h5mu/from_spatialdata_to_h5mu"
   viash_version: "0.9.3"
-  git_commit: "9f2a3e68cb0ae7fc97924d8872376ec7a58afe16"
+  git_commit: "491efceaaf171f50aaa1d28f690c1e974cffc456"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"

target/executable/convert/from_spatialdata_to_h5mu/from_spatialdata_to_h5mu

@@ -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 convert from_spatialdata_to_h5mu"
-LABEL org.opencontainers.image.created="2025-06-11T09:39:26Z"
+LABEL org.opencontainers.image.created="2025-07-10T12:30:14Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="9f2a3e68cb0ae7fc97924d8872376ec7a58afe16"
+LABEL org.opencontainers.image.revision="491efceaaf171f50aaa1d28f690c1e974cffc456"
 LABEL org.opencontainers.image.version="build_main"
 
 VIASHDOCKER

target/executable/convert/from_xenium_to_spatialdata/.config.vsh.yaml

@@ -314,7 +314,7 @@ build_info:
   output: "target/executable/convert/from_xenium_to_spatialdata"
   executable: "target/executable/convert/from_xenium_to_spatialdata/from_xenium_to_spatialdata"
   viash_version: "0.9.3"
-  git_commit: "9f2a3e68cb0ae7fc97924d8872376ec7a58afe16"
+  git_commit: "491efceaaf171f50aaa1d28f690c1e974cffc456"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"

target/executable/convert/from_xenium_to_spatialdata/from_xenium_to_spatialdata

@@ -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 convert from_xenium_to_spatialdata"
-LABEL org.opencontainers.image.created="2025-06-11T09:39:25Z"
+LABEL org.opencontainers.image.created="2025-07-10T12:30:14Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="9f2a3e68cb0ae7fc97924d8872376ec7a58afe16"
+LABEL org.opencontainers.image.revision="491efceaaf171f50aaa1d28f690c1e974cffc456"
 LABEL org.opencontainers.image.version="build_main"
 
 VIASHDOCKER

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

@@ -217,7 +217,7 @@ build_info:
   output: "target/executable/filter/subset_cosmx"
   executable: "target/executable/filter/subset_cosmx/subset_cosmx"
   viash_version: "0.9.3"
-  git_commit: "9f2a3e68cb0ae7fc97924d8872376ec7a58afe16"
+  git_commit: "491efceaaf171f50aaa1d28f690c1e974cffc456"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"

target/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="2025-06-11T09:39:25Z"
+LABEL org.opencontainers.image.created="2025-07-10T12:30:14Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="9f2a3e68cb0ae7fc97924d8872376ec7a58afe16"
+LABEL org.opencontainers.image.revision="491efceaaf171f50aaa1d28f690c1e974cffc456"
 LABEL org.opencontainers.image.version="build_main"
 
 VIASHDOCKER

target/executable/mapping/spaceranger_count/.config.vsh.yaml

@@ -0,0 +1,457 @@
+name: "spaceranger_count"
+namespace: "mapping"
+version: "build_main"
+authors:
+- name: "Jakub Majercik"
+  roles:
+  - "author"
+  info:
+    role: "Contributor"
+    links:
+      email: "jakub@data-intuitive.com"
+      github: "jakubmajercik"
+      linkedin: "jakubmajercik"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Bioinformatics Engineer"
+argument_groups:
+- name: "Inputs"
+  arguments:
+  - type: "file"
+    name: "--gex_reference"
+    description: "Path of folder containing 10x-compatible reference"
+    info: null
+    example:
+    - "/path/to/refdata-gex-GRCh38-2020-A"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--input"
+    description: "Path to a directory containing input FASTQ data. Individual FASTQ\
+      \ files should follow the naming convention of 10x Genomics:\n[Sample Name]_S[Sample\
+      \ Number]_L[Lane Number]_[Read Type]_001.fastq.gz\n\nWhere:\n[Sample Name] is\
+      \ the name assigned during sample preparation/sequencing\nS[Sample Number] is\
+      \ the sample index (usually S1, S2, etc.)\nL[Lane Number] identifies the sequencing\
+      \ lane (L001, L002, etc.)\n\n[Read Type] will be one of:\nR1 - Read 1 (contains\
+      \ the spatial barcode and UMI)\nR2 - Read 2 (contains the actual cDNA sequence)\n\
+      I1 - Index Read 1 (if applicable)\nI2 - Index Read 2 (if applicable)\n"
+    info: null
+    example:
+    - "/path/to/fastq_folder"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--probe_set"
+    description: "CSV file specifying the probe set used"
+    info: null
+    example:
+    - "Visium_Human_Transcriptome_Probe_Set_v2.0_GRCh38-2020-A.csv"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--cytaimage"
+    description: "Brightfield image generated by the CytAssist instrument. \nWhen\
+      \ using CytAssist workflow, either this or --image must be provided.\n"
+    info: null
+    example:
+    - "cyta_image.tif"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--image"
+    description: "H&E or fluorescence microscope image in TIFF or JPG format. \nRequired\
+      \ for standard Visium workflow, optional when using --cytaimage for CytAssist\
+      \ workflow.\n"
+    info: null
+    example:
+    - "brightfield.tif"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--output"
+    description: "The folder to store the alignment results"
+    info: null
+    example:
+    - "/path/to/output"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Slide Information"
+  arguments:
+  - type: "string"
+    name: "--slide"
+    description: "Visium slide serial number (e.g., 'V10J25-015')"
+    info: null
+    example:
+    - "V10J25-015"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--area"
+    description: "Visium capture area identifier (e.g., 'A1')"
+    info: null
+    example:
+    - "A1"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--unknown_slide"
+    description: "Use this option if the slide serial number and area were entered\
+      \ incorrectly on the CytAssist \ninstrument and the correct values are unknown.\
+      \ Not compatible with --slide, --area, or \n--slide-file options\n"
+    info: null
+    required: false
+    choices:
+    - "visium-1"
+    - "visium-2"
+    - "visium-2-large"
+    - "visium-hd"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--slidefile"
+    description: "Slide design file for offline use"
+    info: null
+    example:
+    - "slide_design.gpr"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--override_id"
+    description: "Overrides the slide serial number and capture area provided in the\
+      \ Cytassist image metadata"
+    info: null
+    direction: "input"
+- name: "Image Options"
+  arguments:
+  - type: "file"
+    name: "--darkimage"
+    description: "Multi-channel, dark-background fluorescence image"
+    info: null
+    example:
+    - "fluorescence.tif"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--colorizedimage"
+    description: "Color image representing pre-colored dark-background fluorescence\
+      \ images"
+    info: null
+    example:
+    - "colored_fluorescence.tif"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--dapi_index"
+    description: "Index of DAPI channel (1-indexed) of fluorescence image"
+    info: null
+    example:
+    - 1
+    required: false
+    min: 1
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "double"
+    name: "--image_scale"
+    description: "Microns per microscope image pixel"
+    info: null
+    example:
+    - 0.65
+    required: false
+    min: 0.01
+    max: 10.0
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--reorient_images"
+    description: "Whether to rotate and mirror image to align fiducial pattern"
+    info: null
+    default:
+    - true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Processing Options"
+  arguments:
+  - type: "boolean"
+    name: "--create_bam"
+    description: "Enable or disable BAM file generation"
+    info: null
+    default:
+    - true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--nosecondary"
+    description: "Disable secondary analysis (e.g., clustering)"
+    info: null
+    direction: "input"
+  - type: "integer"
+    name: "--r1_length"
+    description: "Hard trim the input Read 1 to this length before analysis"
+    info: null
+    required: false
+    min: 1
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--r2_length"
+    description: "Hard trim the input Read 2 to this length before analysis"
+    info: null
+    required: false
+    min: 1
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--filter_probes"
+    description: "Whether to filter the probe set using the \"included\" column"
+    info: null
+    default:
+    - true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--custom_bin_size"
+    description: "Bin Visium HD data to specified size in microns (4-100, even values\
+      \ only) in addition to the standard binning size (2 µm, 8 µm, 16 µm)"
+    info: null
+    required: false
+    min: 4
+    max: 100
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Input Selection"
+  arguments:
+  - type: "string"
+    name: "--project"
+    description: "Project folder name within mkfastq output"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--sample"
+    description: "Prefix of FASTQ filenames to select"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--lanes"
+    description: "Only use FASTQs from selected lanes"
+    info: null
+    example:
+    - 1
+    - 2
+    - 3
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
+description: "Count gene expression and protein expression reads from a single capture\
+  \ area."
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "visium"
+- type: "file"
+  path: "GRCh38"
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+repositories:
+- type: "github"
+  name: "openpipeline"
+  repo: "openpipelines-bio/openpipeline"
+  tag: "main_build"
+keywords:
+- "spaceranger"
+links:
+  repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
+  docker_registry: "ghcr.io"
+  documentation: "https://www.10xgenomics.com/support/software/space-ranger/latest/analysis/running-pipelines/space-ranger-count"
+runners:
+- type: "executable"
+  id: "executable"
+  docker_setup_strategy: "ifneedbepullelsecachedbuild"
+- type: "nextflow"
+  id: "nextflow"
+  directives:
+    tag: "$id"
+  auto:
+    simplifyInput: true
+    simplifyOutput: false
+    transcript: false
+    publish: false
+  config:
+    labels:
+      mem1gb: "memory = 1000000000.B"
+      mem2gb: "memory = 2000000000.B"
+      mem5gb: "memory = 5000000000.B"
+      mem10gb: "memory = 10000000000.B"
+      mem20gb: "memory = 20000000000.B"
+      mem50gb: "memory = 50000000000.B"
+      mem100gb: "memory = 100000000000.B"
+      mem200gb: "memory = 200000000000.B"
+      mem500gb: "memory = 500000000000.B"
+      mem1tb: "memory = 1000000000000.B"
+      mem2tb: "memory = 2000000000000.B"
+      mem5tb: "memory = 5000000000000.B"
+      mem10tb: "memory = 10000000000000.B"
+      mem20tb: "memory = 20000000000000.B"
+      mem50tb: "memory = 50000000000000.B"
+      mem100tb: "memory = 100000000000000.B"
+      mem200tb: "memory = 200000000000000.B"
+      mem500tb: "memory = 500000000000000.B"
+      mem1gib: "memory = 1073741824.B"
+      mem2gib: "memory = 2147483648.B"
+      mem4gib: "memory = 4294967296.B"
+      mem8gib: "memory = 8589934592.B"
+      mem16gib: "memory = 17179869184.B"
+      mem32gib: "memory = 34359738368.B"
+      mem64gib: "memory = 68719476736.B"
+      mem128gib: "memory = 137438953472.B"
+      mem256gib: "memory = 274877906944.B"
+      mem512gib: "memory = 549755813888.B"
+      mem1tib: "memory = 1099511627776.B"
+      mem2tib: "memory = 2199023255552.B"
+      mem4tib: "memory = 4398046511104.B"
+      mem8tib: "memory = 8796093022208.B"
+      mem16tib: "memory = 17592186044416.B"
+      mem32tib: "memory = 35184372088832.B"
+      mem64tib: "memory = 70368744177664.B"
+      mem128tib: "memory = 140737488355328.B"
+      mem256tib: "memory = 281474976710656.B"
+      mem512tib: "memory = 562949953421312.B"
+      cpu1: "cpus = 1"
+      cpu2: "cpus = 2"
+      cpu5: "cpus = 5"
+      cpu10: "cpus = 10"
+      cpu20: "cpus = 20"
+      cpu50: "cpus = 50"
+      cpu100: "cpus = 100"
+      cpu200: "cpus = 200"
+      cpu500: "cpus = 500"
+      cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
+  debug: false
+  container: "docker"
+engines:
+- type: "docker"
+  id: "docker"
+  image: "ghcr.io/data-intuitive/spaceranger:3.1"
+  target_registry: "images.viash-hub.com"
+  target_tag: "build_main"
+  namespace_separator: "/"
+  setup:
+  - type: "docker"
+    run:
+    - "DEBIAN_FRONTEND=noninteractive apt update && \\\napt upgrade -y && apt install\
+      \ -y procps && rm -rf /var/lib/apt/lists/*\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/mapping/spaceranger_count/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/mapping/spaceranger_count"
+  executable: "target/executable/mapping/spaceranger_count/spaceranger_count"
+  viash_version: "0.9.3"
+  git_commit: "491efceaaf171f50aaa1d28f690c1e974cffc456"
+  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
+package_config:
+  name: "openpipeline_spatial"
+  version: "build_main"
+  info:
+    test_resources:
+    - type: "s3"
+      path: "s3://openpipelines-bio/openpipeline_spatial/resources_test"
+      dest: "resources_test"
+  repositories:
+  - type: "github"
+    name: "openpipeline"
+    repo: "openpipelines-bio/openpipeline"
+    tag: "main_build"
+  viash_version: "0.9.3"
+  source: "src"
+  target: "target"
+  config_mods:
+  - ".resources += {path: '/src/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 := 'build_main'"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
+    docker_registry: "ghcr.io"

target/executable/mapping/spaceranger_count/nextflow_labels.config

@@ -0,0 +1,68 @@
+process {
+  // Default resources for components that hardly do any processing
+  memory = { 2.GB * task.attempt }
+  cpus = 1
+
+  // Retry for exit codes that have something to do with memory issues
+  errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
+  maxRetries = 3
+  maxMemory = null
+
+  // CPU resources
+  withLabel: singlecpu { cpus = 1 }
+  withLabel: lowcpu { cpus = 4 }
+  withLabel: midcpu { cpus = 10 }
+  withLabel: highcpu { cpus = 20 }
+  
+  // Memory resources
+  withLabel: lowmem { memory = { get_memory( 50.GB * task.attempt ) } }
+  withLabel: midmem { memory = { get_memory( 50.GB * task.attempt ) } }
+  withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
+
+  // Disk space
+  // Nextflow apparently can't handle empty directives, i.e.
+  // withLabel: lowdisk {}
+  // so for that reason we have to add a dummy directive
+  withLabel: lowdisk {
+    dummyDirective = "dummyValue"
+  }
+  withLabel: middisk {
+    dummyDirective = "dummyValue"
+  }
+  withLabel: highdisk {
+    dummyDirective = "dummyValue"
+  }
+  withLabel: veryhighdisk {
+    dummyDirective = "dummyValue"
+  }
+  // NOTE: The above labels intentionally do not have an effect by default.
+  // The user should set the disk space requirements by adding the following
+  // to the compute environment:
+  //
+  // withLabel: lowdisk { disk = { 20.GB * task.attempt } }
+  // withLabel: middisk { disk = { 100.GB * task.attempt } }
+  // withLabel: highdisk { disk = { 200.GB * task.attempt } }
+  // withLabel: veryhighdisk { disk = { 500.GB * task.attempt } }
+}
+
+def get_memory(to_compare) {
+  if (!process.containsKey("maxMemory") || !process.maxMemory) {
+    return to_compare
+  }
+
+  try {
+    if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
+      return process.maxMemory
+    }
+    else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
+      return max_memory as nextflow.util.MemoryUnit
+    }
+    else {
+      return to_compare
+    }  
+  } catch (all) {
+        println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
+        System.exit(1)
+  }
+}

target/nextflow/convert/from_cosmx_to_h5mu/.config.vsh.yaml

@@ -231,7 +231,7 @@ build_info:
   output: "target/nextflow/convert/from_cosmx_to_h5mu"
   executable: "target/nextflow/convert/from_cosmx_to_h5mu/main.nf"
   viash_version: "0.9.3"
-  git_commit: "9f2a3e68cb0ae7fc97924d8872376ec7a58afe16"
+  git_commit: "491efceaaf171f50aaa1d28f690c1e974cffc456"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"

target/nextflow/convert/from_cosmx_to_h5mu/main.nf

@@ -3340,7 +3340,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/convert/from_cosmx_to_h5mu",
     "viash_version" : "0.9.3",
-    "git_commit" : "9f2a3e68cb0ae7fc97924d8872376ec7a58afe16",
+    "git_commit" : "491efceaaf171f50aaa1d28f690c1e974cffc456",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
   },
   "package_config" : {

target/nextflow/convert/from_spatialdata_to_h5mu/.config.vsh.yaml

@@ -217,7 +217,7 @@ build_info:
   output: "target/nextflow/convert/from_spatialdata_to_h5mu"
   executable: "target/nextflow/convert/from_spatialdata_to_h5mu/main.nf"
   viash_version: "0.9.3"
-  git_commit: "9f2a3e68cb0ae7fc97924d8872376ec7a58afe16"
+  git_commit: "491efceaaf171f50aaa1d28f690c1e974cffc456"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"

target/nextflow/convert/from_spatialdata_to_h5mu/main.nf

@@ -3332,7 +3332,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/convert/from_spatialdata_to_h5mu",
     "viash_version" : "0.9.3",
-    "git_commit" : "9f2a3e68cb0ae7fc97924d8872376ec7a58afe16",
+    "git_commit" : "491efceaaf171f50aaa1d28f690c1e974cffc456",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
   },
   "package_config" : {

target/nextflow/convert/from_xenium_to_spatialdata/.config.vsh.yaml

@@ -314,7 +314,7 @@ build_info:
   output: "target/nextflow/convert/from_xenium_to_spatialdata"
   executable: "target/nextflow/convert/from_xenium_to_spatialdata/main.nf"
   viash_version: "0.9.3"
-  git_commit: "9f2a3e68cb0ae7fc97924d8872376ec7a58afe16"
+  git_commit: "491efceaaf171f50aaa1d28f690c1e974cffc456"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"

target/nextflow/convert/from_xenium_to_spatialdata/main.nf

@@ -3430,7 +3430,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/convert/from_xenium_to_spatialdata",
     "viash_version" : "0.9.3",
-    "git_commit" : "9f2a3e68cb0ae7fc97924d8872376ec7a58afe16",
+    "git_commit" : "491efceaaf171f50aaa1d28f690c1e974cffc456",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
   },
   "package_config" : {

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

@@ -217,7 +217,7 @@ build_info:
   output: "target/nextflow/filter/subset_cosmx"
   executable: "target/nextflow/filter/subset_cosmx/main.nf"
   viash_version: "0.9.3"
-  git_commit: "9f2a3e68cb0ae7fc97924d8872376ec7a58afe16"
+  git_commit: "491efceaaf171f50aaa1d28f690c1e974cffc456"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"

target/nextflow/filter/subset_cosmx/main.nf

@@ -3322,7 +3322,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/filter/subset_cosmx",
     "viash_version" : "0.9.3",
-    "git_commit" : "9f2a3e68cb0ae7fc97924d8872376ec7a58afe16",
+    "git_commit" : "491efceaaf171f50aaa1d28f690c1e974cffc456",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
   },
   "package_config" : {

target/nextflow/mapping/spaceranger_count/.config.vsh.yaml

@@ -0,0 +1,457 @@
+name: "spaceranger_count"
+namespace: "mapping"
+version: "build_main"
+authors:
+- name: "Jakub Majercik"
+  roles:
+  - "author"
+  info:
+    role: "Contributor"
+    links:
+      email: "jakub@data-intuitive.com"
+      github: "jakubmajercik"
+      linkedin: "jakubmajercik"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Bioinformatics Engineer"
+argument_groups:
+- name: "Inputs"
+  arguments:
+  - type: "file"
+    name: "--gex_reference"
+    description: "Path of folder containing 10x-compatible reference"
+    info: null
+    example:
+    - "/path/to/refdata-gex-GRCh38-2020-A"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--input"
+    description: "Path to a directory containing input FASTQ data. Individual FASTQ\
+      \ files should follow the naming convention of 10x Genomics:\n[Sample Name]_S[Sample\
+      \ Number]_L[Lane Number]_[Read Type]_001.fastq.gz\n\nWhere:\n[Sample Name] is\
+      \ the name assigned during sample preparation/sequencing\nS[Sample Number] is\
+      \ the sample index (usually S1, S2, etc.)\nL[Lane Number] identifies the sequencing\
+      \ lane (L001, L002, etc.)\n\n[Read Type] will be one of:\nR1 - Read 1 (contains\
+      \ the spatial barcode and UMI)\nR2 - Read 2 (contains the actual cDNA sequence)\n\
+      I1 - Index Read 1 (if applicable)\nI2 - Index Read 2 (if applicable)\n"
+    info: null
+    example:
+    - "/path/to/fastq_folder"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--probe_set"
+    description: "CSV file specifying the probe set used"
+    info: null
+    example:
+    - "Visium_Human_Transcriptome_Probe_Set_v2.0_GRCh38-2020-A.csv"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--cytaimage"
+    description: "Brightfield image generated by the CytAssist instrument. \nWhen\
+      \ using CytAssist workflow, either this or --image must be provided.\n"
+    info: null
+    example:
+    - "cyta_image.tif"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--image"
+    description: "H&E or fluorescence microscope image in TIFF or JPG format. \nRequired\
+      \ for standard Visium workflow, optional when using --cytaimage for CytAssist\
+      \ workflow.\n"
+    info: null
+    example:
+    - "brightfield.tif"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--output"
+    description: "The folder to store the alignment results"
+    info: null
+    example:
+    - "/path/to/output"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Slide Information"
+  arguments:
+  - type: "string"
+    name: "--slide"
+    description: "Visium slide serial number (e.g., 'V10J25-015')"
+    info: null
+    example:
+    - "V10J25-015"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--area"
+    description: "Visium capture area identifier (e.g., 'A1')"
+    info: null
+    example:
+    - "A1"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--unknown_slide"
+    description: "Use this option if the slide serial number and area were entered\
+      \ incorrectly on the CytAssist \ninstrument and the correct values are unknown.\
+      \ Not compatible with --slide, --area, or \n--slide-file options\n"
+    info: null
+    required: false
+    choices:
+    - "visium-1"
+    - "visium-2"
+    - "visium-2-large"
+    - "visium-hd"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--slidefile"
+    description: "Slide design file for offline use"
+    info: null
+    example:
+    - "slide_design.gpr"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--override_id"
+    description: "Overrides the slide serial number and capture area provided in the\
+      \ Cytassist image metadata"
+    info: null
+    direction: "input"
+- name: "Image Options"
+  arguments:
+  - type: "file"
+    name: "--darkimage"
+    description: "Multi-channel, dark-background fluorescence image"
+    info: null
+    example:
+    - "fluorescence.tif"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--colorizedimage"
+    description: "Color image representing pre-colored dark-background fluorescence\
+      \ images"
+    info: null
+    example:
+    - "colored_fluorescence.tif"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--dapi_index"
+    description: "Index of DAPI channel (1-indexed) of fluorescence image"
+    info: null
+    example:
+    - 1
+    required: false
+    min: 1
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "double"
+    name: "--image_scale"
+    description: "Microns per microscope image pixel"
+    info: null
+    example:
+    - 0.65
+    required: false
+    min: 0.01
+    max: 10.0
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--reorient_images"
+    description: "Whether to rotate and mirror image to align fiducial pattern"
+    info: null
+    default:
+    - true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Processing Options"
+  arguments:
+  - type: "boolean"
+    name: "--create_bam"
+    description: "Enable or disable BAM file generation"
+    info: null
+    default:
+    - true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--nosecondary"
+    description: "Disable secondary analysis (e.g., clustering)"
+    info: null
+    direction: "input"
+  - type: "integer"
+    name: "--r1_length"
+    description: "Hard trim the input Read 1 to this length before analysis"
+    info: null
+    required: false
+    min: 1
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--r2_length"
+    description: "Hard trim the input Read 2 to this length before analysis"
+    info: null
+    required: false
+    min: 1
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--filter_probes"
+    description: "Whether to filter the probe set using the \"included\" column"
+    info: null
+    default:
+    - true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--custom_bin_size"
+    description: "Bin Visium HD data to specified size in microns (4-100, even values\
+      \ only) in addition to the standard binning size (2 µm, 8 µm, 16 µm)"
+    info: null
+    required: false
+    min: 4
+    max: 100
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Input Selection"
+  arguments:
+  - type: "string"
+    name: "--project"
+    description: "Project folder name within mkfastq output"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--sample"
+    description: "Prefix of FASTQ filenames to select"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--lanes"
+    description: "Only use FASTQs from selected lanes"
+    info: null
+    example:
+    - 1
+    - 2
+    - 3
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
+description: "Count gene expression and protein expression reads from a single capture\
+  \ area."
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "visium"
+- type: "file"
+  path: "GRCh38"
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+repositories:
+- type: "github"
+  name: "openpipeline"
+  repo: "openpipelines-bio/openpipeline"
+  tag: "main_build"
+keywords:
+- "spaceranger"
+links:
+  repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
+  docker_registry: "ghcr.io"
+  documentation: "https://www.10xgenomics.com/support/software/space-ranger/latest/analysis/running-pipelines/space-ranger-count"
+runners:
+- type: "executable"
+  id: "executable"
+  docker_setup_strategy: "ifneedbepullelsecachedbuild"
+- type: "nextflow"
+  id: "nextflow"
+  directives:
+    tag: "$id"
+  auto:
+    simplifyInput: true
+    simplifyOutput: false
+    transcript: false
+    publish: false
+  config:
+    labels:
+      mem1gb: "memory = 1000000000.B"
+      mem2gb: "memory = 2000000000.B"
+      mem5gb: "memory = 5000000000.B"
+      mem10gb: "memory = 10000000000.B"
+      mem20gb: "memory = 20000000000.B"
+      mem50gb: "memory = 50000000000.B"
+      mem100gb: "memory = 100000000000.B"
+      mem200gb: "memory = 200000000000.B"
+      mem500gb: "memory = 500000000000.B"
+      mem1tb: "memory = 1000000000000.B"
+      mem2tb: "memory = 2000000000000.B"
+      mem5tb: "memory = 5000000000000.B"
+      mem10tb: "memory = 10000000000000.B"
+      mem20tb: "memory = 20000000000000.B"
+      mem50tb: "memory = 50000000000000.B"
+      mem100tb: "memory = 100000000000000.B"
+      mem200tb: "memory = 200000000000000.B"
+      mem500tb: "memory = 500000000000000.B"
+      mem1gib: "memory = 1073741824.B"
+      mem2gib: "memory = 2147483648.B"
+      mem4gib: "memory = 4294967296.B"
+      mem8gib: "memory = 8589934592.B"
+      mem16gib: "memory = 17179869184.B"
+      mem32gib: "memory = 34359738368.B"
+      mem64gib: "memory = 68719476736.B"
+      mem128gib: "memory = 137438953472.B"
+      mem256gib: "memory = 274877906944.B"
+      mem512gib: "memory = 549755813888.B"
+      mem1tib: "memory = 1099511627776.B"
+      mem2tib: "memory = 2199023255552.B"
+      mem4tib: "memory = 4398046511104.B"
+      mem8tib: "memory = 8796093022208.B"
+      mem16tib: "memory = 17592186044416.B"
+      mem32tib: "memory = 35184372088832.B"
+      mem64tib: "memory = 70368744177664.B"
+      mem128tib: "memory = 140737488355328.B"
+      mem256tib: "memory = 281474976710656.B"
+      mem512tib: "memory = 562949953421312.B"
+      cpu1: "cpus = 1"
+      cpu2: "cpus = 2"
+      cpu5: "cpus = 5"
+      cpu10: "cpus = 10"
+      cpu20: "cpus = 20"
+      cpu50: "cpus = 50"
+      cpu100: "cpus = 100"
+      cpu200: "cpus = 200"
+      cpu500: "cpus = 500"
+      cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
+  debug: false
+  container: "docker"
+engines:
+- type: "docker"
+  id: "docker"
+  image: "ghcr.io/data-intuitive/spaceranger:3.1"
+  target_registry: "images.viash-hub.com"
+  target_tag: "build_main"
+  namespace_separator: "/"
+  setup:
+  - type: "docker"
+    run:
+    - "DEBIAN_FRONTEND=noninteractive apt update && \\\napt upgrade -y && apt install\
+      \ -y procps && rm -rf /var/lib/apt/lists/*\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/mapping/spaceranger_count/config.vsh.yaml"
+  runner: "nextflow"
+  engine: "docker|native"
+  output: "target/nextflow/mapping/spaceranger_count"
+  executable: "target/nextflow/mapping/spaceranger_count/main.nf"
+  viash_version: "0.9.3"
+  git_commit: "491efceaaf171f50aaa1d28f690c1e974cffc456"
+  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
+package_config:
+  name: "openpipeline_spatial"
+  version: "build_main"
+  info:
+    test_resources:
+    - type: "s3"
+      path: "s3://openpipelines-bio/openpipeline_spatial/resources_test"
+      dest: "resources_test"
+  repositories:
+  - type: "github"
+    name: "openpipeline"
+    repo: "openpipelines-bio/openpipeline"
+    tag: "main_build"
+  viash_version: "0.9.3"
+  source: "src"
+  target: "target"
+  config_mods:
+  - ".resources += {path: '/src/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 := 'build_main'"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
+    docker_registry: "ghcr.io"

target/nextflow/mapping/spaceranger_count/nextflow.config

@@ -0,0 +1,126 @@
+manifest {
+  name = 'mapping/spaceranger_count'
+  mainScript = 'main.nf'
+  nextflowVersion = '!>=20.12.1-edge'
+  version = 'build_main'
+  description = 'Count gene expression and protein expression reads from a single capture area.'
+  author = 'Jakub Majercik'
+}
+
+process.container = 'nextflow/bash:latest'
+
+// detect tempdir
+tempDir = java.nio.file.Paths.get(
+  System.getenv('NXF_TEMP') ?:
+    System.getenv('VIASH_TEMP') ?: 
+    System.getenv('TEMPDIR') ?: 
+    System.getenv('TMPDIR') ?: 
+    '/tmp'
+).toAbsolutePath()
+
+profiles {
+  no_publish {
+    process {
+      withName: '.*' {
+        publishDir = [
+          enabled: false
+        ]
+      }
+    }
+  }
+  mount_temp {
+    docker.temp            = tempDir
+    podman.temp            = tempDir
+    charliecloud.temp      = tempDir
+  }
+  docker {
+    docker.enabled         = true
+    // docker.userEmulation   = true
+    singularity.enabled    = false
+    podman.enabled         = false
+    shifter.enabled        = false
+    charliecloud.enabled   = false
+  }
+  singularity {
+    singularity.enabled    = true
+    singularity.autoMounts = true
+    docker.enabled         = false
+    podman.enabled         = false
+    shifter.enabled        = false
+    charliecloud.enabled   = false
+  }
+  podman {
+    podman.enabled         = true
+    docker.enabled         = false
+    singularity.enabled    = false
+    shifter.enabled        = false
+    charliecloud.enabled   = false
+  }
+  shifter {
+    shifter.enabled        = true
+    docker.enabled         = false
+    singularity.enabled    = false
+    podman.enabled         = false
+    charliecloud.enabled   = false
+  }
+  charliecloud {
+    charliecloud.enabled   = true
+    docker.enabled         = false
+    singularity.enabled    = false
+    podman.enabled         = false
+    shifter.enabled        = false
+  }
+}
+
+process{
+  withLabel: mem1gb { memory = 1000000000.B }
+  withLabel: mem2gb { memory = 2000000000.B }
+  withLabel: mem5gb { memory = 5000000000.B }
+  withLabel: mem10gb { memory = 10000000000.B }
+  withLabel: mem20gb { memory = 20000000000.B }
+  withLabel: mem50gb { memory = 50000000000.B }
+  withLabel: mem100gb { memory = 100000000000.B }
+  withLabel: mem200gb { memory = 200000000000.B }
+  withLabel: mem500gb { memory = 500000000000.B }
+  withLabel: mem1tb { memory = 1000000000000.B }
+  withLabel: mem2tb { memory = 2000000000000.B }
+  withLabel: mem5tb { memory = 5000000000000.B }
+  withLabel: mem10tb { memory = 10000000000000.B }
+  withLabel: mem20tb { memory = 20000000000000.B }
+  withLabel: mem50tb { memory = 50000000000000.B }
+  withLabel: mem100tb { memory = 100000000000000.B }
+  withLabel: mem200tb { memory = 200000000000000.B }
+  withLabel: mem500tb { memory = 500000000000000.B }
+  withLabel: mem1gib { memory = 1073741824.B }
+  withLabel: mem2gib { memory = 2147483648.B }
+  withLabel: mem4gib { memory = 4294967296.B }
+  withLabel: mem8gib { memory = 8589934592.B }
+  withLabel: mem16gib { memory = 17179869184.B }
+  withLabel: mem32gib { memory = 34359738368.B }
+  withLabel: mem64gib { memory = 68719476736.B }
+  withLabel: mem128gib { memory = 137438953472.B }
+  withLabel: mem256gib { memory = 274877906944.B }
+  withLabel: mem512gib { memory = 549755813888.B }
+  withLabel: mem1tib { memory = 1099511627776.B }
+  withLabel: mem2tib { memory = 2199023255552.B }
+  withLabel: mem4tib { memory = 4398046511104.B }
+  withLabel: mem8tib { memory = 8796093022208.B }
+  withLabel: mem16tib { memory = 17592186044416.B }
+  withLabel: mem32tib { memory = 35184372088832.B }
+  withLabel: mem64tib { memory = 70368744177664.B }
+  withLabel: mem128tib { memory = 140737488355328.B }
+  withLabel: mem256tib { memory = 281474976710656.B }
+  withLabel: mem512tib { memory = 562949953421312.B }
+  withLabel: cpu1 { cpus = 1 }
+  withLabel: cpu2 { cpus = 2 }
+  withLabel: cpu5 { cpus = 5 }
+  withLabel: cpu10 { cpus = 10 }
+  withLabel: cpu20 { cpus = 20 }
+  withLabel: cpu50 { cpus = 50 }
+  withLabel: cpu100 { cpus = 100 }
+  withLabel: cpu200 { cpus = 200 }
+  withLabel: cpu500 { cpus = 500 }
+  withLabel: cpu1000 { cpus = 1000 }
+}
+
+includeConfig("nextflow_labels.config")

target/nextflow/mapping/spaceranger_count/nextflow_labels.config

@@ -0,0 +1,68 @@
+process {
+  // Default resources for components that hardly do any processing
+  memory = { 2.GB * task.attempt }
+  cpus = 1
+
+  // Retry for exit codes that have something to do with memory issues
+  errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
+  maxRetries = 3
+  maxMemory = null
+
+  // CPU resources
+  withLabel: singlecpu { cpus = 1 }
+  withLabel: lowcpu { cpus = 4 }
+  withLabel: midcpu { cpus = 10 }
+  withLabel: highcpu { cpus = 20 }
+  
+  // Memory resources
+  withLabel: lowmem { memory = { get_memory( 50.GB * task.attempt ) } }
+  withLabel: midmem { memory = { get_memory( 50.GB * task.attempt ) } }
+  withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
+
+  // Disk space
+  // Nextflow apparently can't handle empty directives, i.e.
+  // withLabel: lowdisk {}
+  // so for that reason we have to add a dummy directive
+  withLabel: lowdisk {
+    dummyDirective = "dummyValue"
+  }
+  withLabel: middisk {
+    dummyDirective = "dummyValue"
+  }
+  withLabel: highdisk {
+    dummyDirective = "dummyValue"
+  }
+  withLabel: veryhighdisk {
+    dummyDirective = "dummyValue"
+  }
+  // NOTE: The above labels intentionally do not have an effect by default.
+  // The user should set the disk space requirements by adding the following
+  // to the compute environment:
+  //
+  // withLabel: lowdisk { disk = { 20.GB * task.attempt } }
+  // withLabel: middisk { disk = { 100.GB * task.attempt } }
+  // withLabel: highdisk { disk = { 200.GB * task.attempt } }
+  // withLabel: veryhighdisk { disk = { 500.GB * task.attempt } }
+}
+
+def get_memory(to_compare) {
+  if (!process.containsKey("maxMemory") || !process.maxMemory) {
+    return to_compare
+  }
+
+  try {
+    if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
+      return process.maxMemory
+    }
+    else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
+      return max_memory as nextflow.util.MemoryUnit
+    }
+    else {
+      return to_compare
+    }  
+  } catch (all) {
+        println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
+        System.exit(1)
+  }
+}

target/nextflow/mapping/spaceranger_count/nextflow_schema.json

@@ -0,0 +1,237 @@
+{
+  "$schema": "https://json-schema.org/draft/2020-12/schema",
+  "title": "spaceranger_count",
+  "description": "Count gene expression and protein expression reads from a single capture area.",
+  "type": "object",
+  "$defs": {
+    "inputs": {
+      "title": "Inputs",
+      "type": "object",
+      "description": "No description",
+      "properties": {
+        "gex_reference": {
+          "type": "string",
+          "format": "path",
+          "exists": true,
+          "description": "Path of folder containing 10x-compatible reference",
+          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"/path/to/refdata-gex-GRCh38-2020-A\"`. "
+        },
+        "input": {
+          "type": "string",
+          "format": "path",
+          "exists": true,
+          "description": "Path to a directory containing input FASTQ data",
+          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"/path/to/fastq_folder\"`. "
+        },
+        "probe_set": {
+          "type": "string",
+          "format": "path",
+          "exists": true,
+          "description": "CSV file specifying the probe set used",
+          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"Visium_Human_Transcriptome_Probe_Set_v2.0_GRCh38-2020-A.csv\"`. "
+        },
+        "cytaimage": {
+          "type": "string",
+          "format": "path",
+          "description": "Brightfield image generated by the CytAssist instrument",
+          "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"cyta_image.tif\"`. "
+        },
+        "image": {
+          "type": "string",
+          "format": "path",
+          "description": "H&E or fluorescence microscope image in TIFF or JPG format",
+          "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"brightfield.tif\"`. "
+        }
+      }
+    },
+    "outputs": {
+      "title": "Outputs",
+      "type": "object",
+      "description": "No description",
+      "properties": {
+        "output": {
+          "type": "string",
+          "format": "path",
+          "description": "The folder to store the alignment results",
+          "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output\"`, direction: `output`, example: `\"/path/to/output\"`. ",
+          "default": "$id.$key.output"
+        }
+      }
+    },
+    "slide information": {
+      "title": "Slide Information",
+      "type": "object",
+      "description": "No description",
+      "properties": {
+        "slide": {
+          "type": "string",
+          "description": "Visium slide serial number (e.g., 'V10J25-015')",
+          "help_text": "Type: `string`, multiple: `False`, example: `\"V10J25-015\"`. "
+        },
+        "area": {
+          "type": "string",
+          "description": "Visium capture area identifier (e.g., 'A1')",
+          "help_text": "Type: `string`, multiple: `False`, example: `\"A1\"`. "
+        },
+        "unknown_slide": {
+          "type": "string",
+          "description": "Use this option if the slide serial number and area were entered incorrectly on the CytAssist \ninstrument and the correct values are unknown",
+          "help_text": "Type: `string`, multiple: `False`, choices: ``visium-1`, `visium-2`, `visium-2-large`, `visium-hd``. ",
+          "enum": [
+            "visium-1",
+            "visium-2",
+            "visium-2-large",
+            "visium-hd"
+          ]
+        },
+        "slidefile": {
+          "type": "string",
+          "format": "path",
+          "description": "Slide design file for offline use",
+          "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"slide_design.gpr\"`. "
+        },
+        "override_id": {
+          "type": "boolean",
+          "description": "Overrides the slide serial number and capture area provided in the Cytassist image metadata",
+          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
+          "default": false
+        }
+      }
+    },
+    "image options": {
+      "title": "Image Options",
+      "type": "object",
+      "description": "No description",
+      "properties": {
+        "darkimage": {
+          "type": "string",
+          "format": "path",
+          "description": "Multi-channel, dark-background fluorescence image",
+          "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"fluorescence.tif\"`. "
+        },
+        "colorizedimage": {
+          "type": "string",
+          "format": "path",
+          "description": "Color image representing pre-colored dark-background fluorescence images",
+          "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"colored_fluorescence.tif\"`. "
+        },
+        "dapi_index": {
+          "type": "integer",
+          "description": "Index of DAPI channel (1-indexed) of fluorescence image",
+          "help_text": "Type: `integer`, multiple: `False`, example: `1`. "
+        },
+        "image_scale": {
+          "type": "number",
+          "description": "Microns per microscope image pixel",
+          "help_text": "Type: `double`, multiple: `False`, example: `0.65`. "
+        },
+        "reorient_images": {
+          "type": "boolean",
+          "description": "Whether to rotate and mirror image to align fiducial pattern",
+          "help_text": "Type: `boolean`, multiple: `False`, default: `true`. ",
+          "default": true
+        }
+      }
+    },
+    "processing options": {
+      "title": "Processing Options",
+      "type": "object",
+      "description": "No description",
+      "properties": {
+        "create_bam": {
+          "type": "boolean",
+          "description": "Enable or disable BAM file generation",
+          "help_text": "Type: `boolean`, multiple: `False`, required, default: `true`. ",
+          "default": true
+        },
+        "nosecondary": {
+          "type": "boolean",
+          "description": "Disable secondary analysis (e.g., clustering)",
+          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
+          "default": false
+        },
+        "r1_length": {
+          "type": "integer",
+          "description": "Hard trim the input Read 1 to this length before analysis",
+          "help_text": "Type: `integer`, multiple: `False`. "
+        },
+        "r2_length": {
+          "type": "integer",
+          "description": "Hard trim the input Read 2 to this length before analysis",
+          "help_text": "Type: `integer`, multiple: `False`. "
+        },
+        "filter_probes": {
+          "type": "boolean",
+          "description": "Whether to filter the probe set using the \"included\" column",
+          "help_text": "Type: `boolean`, multiple: `False`, default: `true`. ",
+          "default": true
+        },
+        "custom_bin_size": {
+          "type": "integer",
+          "description": "Bin Visium HD data to specified size in microns (4-100, even values only) in addition to the standard binning size (2 µm, 8 µm, 16 µm)",
+          "help_text": "Type: `integer`, multiple: `False`. "
+        }
+      }
+    },
+    "input selection": {
+      "title": "Input Selection",
+      "type": "object",
+      "description": "No description",
+      "properties": {
+        "project": {
+          "type": "string",
+          "description": "Project folder name within mkfastq output",
+          "help_text": "Type: `string`, multiple: `False`. "
+        },
+        "sample": {
+          "type": "string",
+          "description": "Prefix of FASTQ filenames to select",
+          "help_text": "Type: `string`, multiple: `False`. "
+        },
+        "lanes": {
+          "type": "array",
+          "items": {
+            "type": "integer"
+          },
+          "description": "Only use FASTQs from selected lanes",
+          "help_text": "Type: `integer`, multiple: `True`, example: `[1;2;3]`. "
+        }
+      }
+    },
+    "nextflow input-output arguments": {
+      "title": "Nextflow input-output arguments",
+      "type": "object",
+      "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
+      "properties": {
+        "publish_dir": {
+          "type": "string",
+          "description": "Path to an output directory.",
+          "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. "
+        }
+      }
+    }
+  },
+  "allOf": [
+    {
+      "$ref": "#/$defs/inputs"
+    },
+    {
+      "$ref": "#/$defs/outputs"
+    },
+    {
+      "$ref": "#/$defs/slide information"
+    },
+    {
+      "$ref": "#/$defs/image options"
+    },
+    {
+      "$ref": "#/$defs/processing options"
+    },
+    {
+      "$ref": "#/$defs/input selection"
+    },
+    {
+      "$ref": "#/$defs/nextflow input-output arguments"
+    }
+  ]
+}