Merge pull request #84 from PixelgenTechnologies/EXE-1100-prepping-fo…

…r-pixelator-0.16

Update to pixelator 0.16.2

CHANGELOG.md

@@ -3,6 +3,25 @@
 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).
 
+## [UNRELEASED] - YYYY-MM-DD
+
+### Changed
+
+- `collapse` and `graph` steps output parquet files
+- Update pixelator to 0.16.2
+
+### Software dependencies
+
+| Dependency  | Old version | New version |
+| ----------- | ----------- | ----------- |
+| `pixelator` | 0.15.2      | 0.16.2      |
+
+> **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.
+
 ## [[1.0.3](https://github.com/nf-core/pixelator/releases/tag/1.0.3)] - 2024-01-19
 
 ### Enhancements & fixes

docs/output.md

@@ -110,7 +110,7 @@ given barcodes/antibodies.
 
   - `collapse`
 
-    - `<sample-id>.collapsed.csv.gz`: Edgelist of the graph.
+    - `<sample-id>.collapsed.parquet`: Edgelist of the graph.
     - `<sample-id>.report.json`: Statistics for the collapse step.
     - `<sample-id>.meta.json`: Command invocation metadata.
 
@@ -137,10 +137,8 @@ The output format of this command is an edge list in CSV format.
 
   - `graph`
 
-    - `<sample-id>.edgelist.csv.gz`:
-      Edge list dataframe (CSV) after recovering technical multiplets.
-    - `<sample-id>.raw_edgelist.csv.gz`:
-      Raw edge list dataframe in csv format before recovering technical multiplets.
+    - `<sample-id>.edgelist.parquet`:
+      Edge list dataframe after recovering technical multiplets.
     - `<sample-id>.components_recovered.csv`:
       List of new components recovered (when using `--multiple-recovery`)
     - `<sample-id>.meta.json`: Command invocation metadata.

modules/local/pixelator/collect_metadata.nf

@@ -6,10 +6,10 @@ process PIXELATOR_COLLECT_METADATA {
     label 'process_single'
     cache false
 
-    conda "bioconda::pixelator=0.15.2"
+    conda "bioconda::pixelator=0.16.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pixelator:0.15.2--pyh7cba7a3_0' :
-        'biocontainers/pixelator:0.15.2--pyh7cba7a3_0' }"
+        'https://depot.galaxyproject.org/singularity/pixelator:0.16.2--pyhdfd78af_0' :
+        'biocontainers/pixelator:0.16.2--pyhdfd78af_0' }"
 
     input:
 

modules/local/pixelator/list_options.nf

@@ -2,10 +2,10 @@ process PIXELATOR_LIST_OPTIONS {
     label 'process_single'
 
 
-    conda "bioconda::pixelator=0.15.2"
+    conda "bioconda::pixelator=0.16.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pixelator:0.15.2--pyh7cba7a3_0' :
-        'biocontainers/pixelator:0.15.2--pyh7cba7a3_0' }"
+        'https://depot.galaxyproject.org/singularity/pixelator:0.16.2--pyhdfd78af_0' :
+        'biocontainers/pixelator:0.16.2--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=0.15.2"
+    conda "bioconda::pixelator=0.16.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pixelator:0.15.2--pyh7cba7a3_0' :
-        'biocontainers/pixelator:0.15.2--pyh7cba7a3_0' }"
+        'https://depot.galaxyproject.org/singularity/pixelator:0.16.2--pyhdfd78af_0' :
+        'biocontainers/pixelator:0.16.2--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(reads)

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

@@ -3,10 +3,10 @@ process PIXELATOR_ANALYSIS {
     label 'process_medium'
 
 
-    conda "bioconda::pixelator=0.15.2"
+    conda "bioconda::pixelator=0.16.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pixelator:0.15.2--pyh7cba7a3_0' :
-        'biocontainers/pixelator:0.15.2--pyh7cba7a3_0' }"
+        'https://depot.galaxyproject.org/singularity/pixelator:0.16.2--pyhdfd78af_0' :
+        'biocontainers/pixelator:0.16.2--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=0.15.2"
+    conda "bioconda::pixelator=0.16.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pixelator:0.15.2--pyh7cba7a3_0' :
-        'biocontainers/pixelator:0.15.2--pyh7cba7a3_0' }"
+        'https://depot.galaxyproject.org/singularity/pixelator:0.16.2--pyhdfd78af_0' :
+        'biocontainers/pixelator:0.16.2--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(dataset), path(panel_file), val(panel)

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

@@ -2,21 +2,21 @@ process PIXELATOR_COLLAPSE {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::pixelator=0.15.2"
+    conda "bioconda::pixelator=0.16.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pixelator:0.15.2--pyh7cba7a3_0' :
-        'biocontainers/pixelator:0.15.2--pyh7cba7a3_0' }"
+        'https://depot.galaxyproject.org/singularity/pixelator:0.16.2--pyhdfd78af_0' :
+        'biocontainers/pixelator:0.16.2--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(reads), path(panel_file), val(panel)
 
     output:
-    tuple val(meta), path("collapse/*.collapsed.csv.gz"), emit: collapsed
-    tuple val(meta), path("collapse/*.report.json")     , emit: report_json
-    tuple val(meta), path("collapse/*.meta.json")       , emit: metadata
-    tuple val(meta), path("*pixelator-collapse.log")    , emit: log
+    tuple val(meta), path("collapse/*.collapsed.parquet"), emit: collapsed
+    tuple val(meta), path("collapse/*.report.json")      , emit: report_json
+    tuple val(meta), path("collapse/*.meta.json")        , emit: metadata
+    tuple val(meta), path("*pixelator-collapse.log")     , emit: log
 
-    path "versions.yml"                                 , emit: versions
+    path "versions.yml"                                  , emit: versions
 
     when:
     task.ext.when == null || task.ext.when

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

@@ -3,10 +3,10 @@ process PIXELATOR_DEMUX {
     label 'process_medium'
 
 
-    conda "bioconda::pixelator=0.15.2"
+    conda "bioconda::pixelator=0.16.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pixelator:0.15.2--pyh7cba7a3_0' :
-        'biocontainers/pixelator:0.15.2--pyh7cba7a3_0' }"
+        'https://depot.galaxyproject.org/singularity/pixelator:0.16.2--pyhdfd78af_0' :
+        'biocontainers/pixelator:0.16.2--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(reads), path(panel_file), val(panel)

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

@@ -3,17 +3,16 @@ process PIXELATOR_GRAPH {
     label 'process_medium'
 
 
-    conda "bioconda::pixelator=0.15.2"
+    conda "bioconda::pixelator=0.16.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pixelator:0.15.2--pyh7cba7a3_0' :
-        'biocontainers/pixelator:0.15.2--pyh7cba7a3_0' }"
+        'https://depot.galaxyproject.org/singularity/pixelator:0.16.2--pyhdfd78af_0' :
+        'biocontainers/pixelator:0.16.2--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(edge_list)
 
     output:
-    tuple val(meta), path("graph/*.edgelist.csv.gz")         , emit: edgelist
-    tuple val(meta), path("graph/*.raw_edgelist.csv.gz")     , emit: raw_edgelist
+    tuple val(meta), path("graph/*.edgelist.parquet")         , emit: edgelist
     tuple val(meta), path("graph/*.components_recovered.csv"), emit: components_recovered, optional: true
     tuple val(meta), path("graph/*.report.json")             , emit: report_json
     tuple val(meta), path("graph/*.meta.json")               , emit: input_params

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

@@ -3,10 +3,10 @@ process PIXELATOR_QC {
     label 'process_medium'
 
 
-    conda "bioconda::pixelator=0.15.2"
+    conda "bioconda::pixelator=0.16.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pixelator:0.15.2--pyh7cba7a3_0' :
-        'biocontainers/pixelator:0.15.2--pyh7cba7a3_0' }"
+        'https://depot.galaxyproject.org/singularity/pixelator:0.16.2--pyhdfd78af_0' :
+        'biocontainers/pixelator:0.16.2--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=0.15.2"
+    conda "bioconda::pixelator=0.16.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pixelator:0.15.2--pyh7cba7a3_0' :
-        'biocontainers/pixelator:0.15.2--pyh7cba7a3_0' }"
+        'https://depot.galaxyproject.org/singularity/pixelator:0.16.2--pyhdfd78af_0' :
+        'biocontainers/pixelator:0.16.2--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(panel_file), val(panel)