Feature/exe 1732 update to pixelator 0.17.1

CHANGELOG.md

@@ -3,6 +3,26 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [[1.2.0](https://github.com/nf-core/pixelator/releases/tag/1.1.0)] - 2024-05-??
+
+### Enhancements & fixes
+
+- [[PR #90](https://github.com/nf-core/pixelator/pull/90)] - Update pixelator to 0.17.1
+- [[PR #90](https://github.com/nf-core/pixelator/pull/90)] - Add `pixelator single-cell layout` command
+- [[PR #90](https://github.com/nf-core/pixelator/pull/90)] - `graph` step is now using `process_high` as it's resource tag
+
+### Software dependencies
+
+| Dependency  | Old version | New version |
+| ----------- | ----------- | ----------- |
+| `pixelator` | 0.16.2      | 0.17.1      |
+
+> **NB:** Dependency has been **updated** if both old and new version information is present.
+>
+> **NB:** Dependency has been **added** if just the new version information is present.
+>
+> **NB:** Dependency has been **removed** if new version information isn't present.
+
 ## [[1.1.0](https://github.com/nf-core/pixelator/releases/tag/1.1.0)] - 2024-03-29
 
 ### Enhancements & fixes

conf/modules.config

@@ -133,15 +133,25 @@ process {
             params.compute_polarization ? "--compute-polarization" : '',
             params.compute_colocalization ? "--compute-colocalization" : '',
             params.use_full_bipartite ? "--use-full-bipartite " : '',
-            params.polarization_normalization ? "--polarization-normalization ${params.polarization_normalization}" : '',
-            params.polarization_binarization ? "--polarization-binarization" : '',
+            params.polarization_min_marker_count ? "--polarization-min-marker-count ${params.polarization_min_marker_count}" : '',
+            params.polarization_transformation ? "--polarization-transformation ${params.polarization_transformation}" : '',
             params.colocalization_transformation ? "--colocalization-transformation ${params.colocalization_transformation}" : '',
+            params.polarization_n_permutations ? "--polarization-n-permutations ${params.polarization_n_permutations}" : '',
             (params.colocalization_neighbourhood_size instanceof Integer) ? "--colocalization-neighbourhood-size ${params.colocalization_neighbourhood_size}" : '',
             (params.colocalization_n_permutations instanceof Integer) ? "--colocalization-n-permutations ${params.colocalization_n_permutations}" : '',
             (params.colocalization_min_region_count instanceof Integer) ? "--colocalization-min-region-count ${params.colocalization_min_region_count}" : '',
         ].join(' ').trim()
     }
 
+    withName: PIXELATOR_LAYOUT {
+        ext.when = { !params.skip_layout }
+        ext.args = [
+            params.no_node_marker_counts ? "--no-node-marker-counts" : '',
+            params.layout_algorithm ? "--layout-algorithm ${params.layout_algorithm} " : '',
+        ].join(' ').trim()
+    }
+
+
     withName: PIXELATOR_REPORT {
         ext.when = { !params.skip_report }
     }

conf/test.config

@@ -34,4 +34,10 @@ params {
     colocalization_min_region_count = 0
     colocalization_n_permutations = 10
     colocalization_neighbourhood_size = 1
+
+    // For now skip the layout step since it is very slow on these
+    // small test datasets
+    skip_layout = true
+    // using this since the default pmds_3d does not work on very small graphs
+    layout_algorithm = "fruchterman_reingold_3d"
 }

docs/output.md

@@ -168,7 +168,7 @@ newly recovered components are stored in a file (components_recovered.csv).
 - `pixelator`
 
   - `annotate`
-    - `<sample-id>.dataset.pxl`
+    - `<sample-id>.annotated.dataset.pxl`
     - `<sample-id>.meta.json`: Command invocation metadata.
     - `<sample-id>.rank_vs_size.png`
     - `<sample-id>.raw_components_metrics.csv`
@@ -193,7 +193,7 @@ edgelist to find putative cells, and it will generate a pxl file containing the
 
   - `analysis`
 
-    - `<sample-id>.dataset.pxl`: PXL file with the analysis results added to it.
+    - `<sample-id>.analysis.dataset.pxl`: PXL file with the analysis results added to it.
     - `<sample-id>.meta.json`: Command invocation metadata.
     - `<sample-id>.report.json`: Statistics for the analysis step.
 
@@ -214,6 +214,30 @@ Currently, the following analysis are performed:
 Each analysis can be disabled by using respectively `--compute_polarization false` or `--compute_colocalization false`.
 This entire step can also be skipped using the `--skip_analysis` option.
 
+### Compute layouts for visualization
+
+<details markdown="1">
+<summary>Output files</summary>
+
+- `pixelator`
+
+  - `layout`
+
+    - `<sample-id>.layout.dataset.pxl`: PXL file with the layout results added to it.
+    - `<sample-id>.meta.json`: Command invocation metadata.
+    - `<sample-id>.report.json`: Statistics for the layout step.
+
+  - `logs`
+    - `<sample-id>.pixelator-layout.log`: pixelator log output.
+
+</details>
+
+This step uses the `pixelator single-cell layout` command.
+It will generate precomputed layouts that can be used to visualize cells
+as part of the downstream analysis.
+
+This entire step can also be skipped using the `--skip_layout` option.
+
 ### Generate reports
 
 <details markdown="1">

modules/local/pixelator/collect_metadata.nf

@@ -6,10 +6,10 @@ process PIXELATOR_COLLECT_METADATA {
     label 'process_single'
     cache false
 
-    conda "bioconda::pixelator=0.16.2"
+    conda "bioconda::pixelator=0.17.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pixelator:0.16.2--pyhdfd78af_0' :
-        'biocontainers/pixelator:0.16.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/pixelator:0.17.1--pyhdfd78af_0' :
+        'biocontainers/pixelator:0.17.1--pyhdfd78af_0' }"
 
     input:
 

modules/local/pixelator/list_options.nf

@@ -2,10 +2,10 @@ process PIXELATOR_LIST_OPTIONS {
     label 'process_single'
 
 
-    conda "bioconda::pixelator=0.16.2"
+    conda "bioconda::pixelator=0.17.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pixelator:0.16.2--pyhdfd78af_0' :
-        'biocontainers/pixelator:0.16.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/pixelator:0.17.1--pyhdfd78af_0' :
+        'biocontainers/pixelator:0.17.1--pyhdfd78af_0' }"
 
     output:
     path "design_options.txt"     , emit: designs

modules/local/pixelator/single-cell/amplicon/main.nf

@@ -3,10 +3,10 @@ process PIXELATOR_AMPLICON {
     label 'process_low'
 
 
-    conda "bioconda::pixelator=0.16.2"
+    conda "bioconda::pixelator=0.17.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pixelator:0.16.2--pyhdfd78af_0' :
-        'biocontainers/pixelator:0.16.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/pixelator:0.17.1--pyhdfd78af_0' :
+        'biocontainers/pixelator:0.17.1--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(reads)

modules/local/pixelator/single-cell/analysis/main.nf

@@ -2,11 +2,10 @@ process PIXELATOR_ANALYSIS {
     tag "$meta.id"
     label 'process_medium'
 
-
-    conda "bioconda::pixelator=0.16.2"
+    conda "bioconda::pixelator=0.17.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pixelator:0.16.2--pyhdfd78af_0' :
-        'biocontainers/pixelator:0.16.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/pixelator:0.17.1--pyhdfd78af_0' :
+        'biocontainers/pixelator:0.17.1--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(data)

modules/local/pixelator/single-cell/annotate/main.nf

@@ -3,10 +3,10 @@ process PIXELATOR_ANNOTATE {
     label 'process_medium'
 
 
-    conda "bioconda::pixelator=0.16.2"
+    conda "bioconda::pixelator=0.17.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pixelator:0.16.2--pyhdfd78af_0' :
-        'biocontainers/pixelator:0.16.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/pixelator:0.17.1--pyhdfd78af_0' :
+        'biocontainers/pixelator:0.17.1--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(dataset), path(panel_file), val(panel)

modules/local/pixelator/single-cell/collapse/main.nf

@@ -2,10 +2,10 @@ process PIXELATOR_COLLAPSE {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::pixelator=0.16.2"
+    conda "bioconda::pixelator=0.17.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pixelator:0.16.2--pyhdfd78af_0' :
-        'biocontainers/pixelator:0.16.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/pixelator:0.17.1--pyhdfd78af_0' :
+        'biocontainers/pixelator:0.17.1--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(reads), path(panel_file), val(panel)

modules/local/pixelator/single-cell/demux/main.nf

@@ -3,10 +3,10 @@ process PIXELATOR_DEMUX {
     label 'process_medium'
 
 
-    conda "bioconda::pixelator=0.16.2"
+    conda "bioconda::pixelator=0.17.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pixelator:0.16.2--pyhdfd78af_0' :
-        'biocontainers/pixelator:0.16.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/pixelator:0.17.1--pyhdfd78af_0' :
+        'biocontainers/pixelator:0.17.1--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(reads), path(panel_file), val(panel)

modules/local/pixelator/single-cell/graph/main.nf

@@ -1,12 +1,12 @@
 process PIXELATOR_GRAPH {
     tag "$meta.id"
-    label 'process_medium'
+    label 'process_high'
 
 
-    conda "bioconda::pixelator=0.16.2"
+    conda "bioconda::pixelator=0.17.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pixelator:0.16.2--pyhdfd78af_0' :
-        'biocontainers/pixelator:0.16.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/pixelator:0.17.1--pyhdfd78af_0' :
+        'biocontainers/pixelator:0.17.1--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(edge_list)

modules/local/pixelator/single-cell/layout/main.nf

@@ -0,0 +1,47 @@
+process PIXELATOR_LAYOUT {
+    tag "$meta.id"
+    label 'process_medium'
+
+
+    conda "bioconda::pixelator=0.17.1"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/pixelator:0.17.1--pyhdfd78af_0' :
+        'biocontainers/pixelator:0.17.1--pyhdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(data)
+
+    output:
+    tuple val(meta), path("layout/*dataset.pxl")  , emit: dataset
+    tuple val(meta), path("layout/*report.json")  , emit: report_json
+    tuple val(meta), path("layout/*.meta.json")   , emit: metadata
+    tuple val(meta), path("layout/*")             , emit: all_results
+    tuple val(meta), path("*pixelator-layout.log"), emit: log
+
+    path "versions.yml"                           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+
+    prefix = task.ext.prefix ?: "${meta.id}"
+    def args = task.ext.args ?: ''
+
+    """
+    pixelator \\
+        --cores $task.cpus \\
+        --log-file ${prefix}.pixelator-layout.log \\
+        --verbose \\
+        single-cell \\
+        layout \\
+        --output . \\
+        $args \\
+        $data
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        pixelator: \$(echo \$(pixelator --version 2>/dev/null) | sed 's/pixelator, version //g' )
+    END_VERSIONS
+    """
+}

modules/local/pixelator/single-cell/qc/main.nf

@@ -3,10 +3,10 @@ process PIXELATOR_QC {
     label 'process_medium'
 
 
-    conda "bioconda::pixelator=0.16.2"
+    conda "bioconda::pixelator=0.17.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pixelator:0.16.2--pyhdfd78af_0' :
-        'biocontainers/pixelator:0.16.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/pixelator:0.17.1--pyhdfd78af_0' :
+        'biocontainers/pixelator:0.17.1--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(reads)

modules/local/pixelator/single-cell/report/main.nf

@@ -3,10 +3,10 @@ process PIXELATOR_REPORT {
     label 'process_low'
 
 
-    conda "bioconda::pixelator=0.16.2"
+    conda "bioconda::pixelator=0.17.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pixelator:0.16.2--pyhdfd78af_0' :
-        'biocontainers/pixelator:0.16.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/pixelator:0.17.1--pyhdfd78af_0' :
+        'biocontainers/pixelator:0.17.1--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(panel_file), val(panel)

nextflow.config

@@ -54,16 +54,22 @@ params {
     compute_polarization = true
     compute_colocalization = true
     use_full_bipartite = false
-    polarization_normalization = "clr"
-    polarization_binarization = false
+    polarization_transformation = "log1p"
+    polarization_min_marker_count = 5
+    polarization_n_permutations = 50
     colocalization_transformation = "log1p"
     colocalization_neighbourhood_size = 1
     colocalization_n_permutations = 50
     colocalization_min_region_count = 5
 
+    // layout options
+    no_node_marker_counts = false
+    layout_algorithm = "pmds_3d"
+
     // skip options
     skip_report   = false
     skip_analysis = false
+    skip_layout   = false
 
     // Main pixelator container override
     pixelator_container        = null

nextflow_schema.json

@@ -256,21 +256,28 @@
                     "description": "Use the bipartite graph instead of the one-node projection when computing polarization, coabundance and colocalization scores",
                     "type": "boolean"
                 },
-                "polarization_normalization": {
-                    "description": "Which approach to use to normalize the antibody counts.",
-                    "help_text": "- `raw`: use the raw counts.\n- `CLR`: use the CLR-transformed counts.\n- `denoise`: use CLR-transformed counts and subtract the counts of control antibodies",
+                "polarization_transformation": {
+                    "description": "Which transformation to use for the antibody counts when calculating polarity scores.",
+                    "help_text": "- `raw`: use the raw counts.\n- `log1p`: use the log1p-transformed counts.\n",
                     "type": "string",
-                    "enum": ["raw", "clr", "denoise"],
-                    "default": "clr"
+                    "enum": ["raw", "log1p"],
+                    "default": "log1p"
                 },
-                "polarization_binarization": {
-                    "fa_icon": "fas binary",
-                    "description": "Transform the antibody counts to 0-1 (binarize) when computing polarization",
-                    "type": "boolean"
+                "polarization_n_permutations": {
+                    "type": "integer",
+                    "description": "Set the number of permutations use to compute the empirical z- and p-values for the polarity score",
+                    "default": 50,
+                    "minimum": 5
+                },
+                "polarization_min_marker_count": {
+                    "type": "integer",
+                    "description": "The minimum number of counts of a marker to calculate the polarity score in the component",
+                    "default": 5,
+                    "minimum": 2
                 },
                 "colocalization_transformation": {
                     "type": "string",
-                    "enum": ["raw", "clr", "log1p", "relative"],
+                    "enum": ["raw", "log1p", "rate-diff"],
                     "default": "log1p",
                     "description": "Select the type of transformation to use on the node by antibody counts matrix when computing colocalization"
                 },
@@ -294,6 +301,27 @@
                 }
             }
         },
+        "layout_options": {
+            "title": "Options for pixelator layout command.",
+            "type": "object",
+            "properties": {
+                "skip_layout": {
+                    "description": "Skip layout step",
+                    "type": "boolean"
+                },
+                "no_node_marker_counts": {
+                    "description": "Skip adding marker counts to the layout.",
+                    "type": "boolean",
+                    "default": false
+                },
+                "layout_algorithm": {
+                    "description": "Select a layout algorithm to use. This can be specified as a comma separated list to compute multiple layouts. Possible values are: fruchterman_reingold, fruchterman_reingold_3d, kamada_kawai, kamada_kawai_3d, pmds, pmds_3d",
+                    "type": "string",
+                    "pattern": "(\\S+)?(,\\S+)*",
+                    "default": "pmds_3d"
+                }
+            }
+        },
         "report_options": {
             "title": "Options for pixelator report command.",
             "type": "object",