Merge pull request #192 from Aratz/patch

Aratz · web-flow · commit 9c79407885cd · 2026-03-09T13:32:23.000+01:00
Patch release v3.0.1
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -23,4 +23,4 @@ template:
     - fastqc
     - multiqc
     - igenomes
-  version: 3.0.0
+  version: 3.0.1
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,12 @@
 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).
 
+## [[3.0.1](https://github.com/nf-core/pixelator/releases/tag/3.0.0)] - 2026-03-09
+
+### Enhancements & fixes
+
+- Fix Issue #191 by @Aratz [#192](https://github.com/nf-core/pixelator/pull/183)
+
 ## [[3.0.0](https://github.com/nf-core/pixelator/releases/tag/3.0.0)] - 2026-02-23
 
 ### Changed
diff --git a/conf/modules.config b/conf/modules.config
@@ -32,10 +32,6 @@ process {
                 pattern: '*.log'
             ]
         ]
-
-        if (params.pixelator_container) {
-            container = params.pixelator_container
-        }
     }
 
     withName: PIXELATOR_LIST_OPTIONS {
@@ -45,10 +41,4 @@ process {
     withName: "CAT_FASTQ" {
         publishDir = [ enabled: false ]
     }
-
-    withName: "EXPERIMENT_SUMMARY" {
-        if (params.experiment_summary_container) {
-            container = params.experiment_summary_container
-        }
-    }
 }
diff --git a/modules/local/experiment_summary/main.nf b/modules/local/experiment_summary/main.nf
@@ -2,7 +2,7 @@ process EXPERIMENT_SUMMARY {
     tag "${meta.id}"
     label "process_medium"
 
-    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+    container "${params.experiment_summary_container?: workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
         ? 'quay.io/pixelgen-technologies/pixelatores:0.6.0'
         : 'quay.io/pixelgen-technologies/pixelatores:0.6.0'}"
 
diff --git a/modules/local/pixelator/list_options/main.nf b/modules/local/pixelator/list_options/main.nf
@@ -4,7 +4,7 @@ process PIXELATOR_LIST_OPTIONS {
 
     // TODO: Add conda back
     // conda "${moduleDir}/environment.yml"
-    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+    container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
         ? 'quay.io/pixelgen-technologies/pixelator:0.23.0'
         : 'quay.io/pixelgen-technologies/pixelator:0.23.0'}"
 
diff --git a/modules/local/pixelator/single-cell-pna/amplicon/main.nf b/modules/local/pixelator/single-cell-pna/amplicon/main.nf
@@ -4,7 +4,7 @@ process PIXELATOR_PNA_AMPLICON {
 
     // TODO: Add conda
     // conda "bioconda::pixelator=0.18.2"
-    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+    container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
         ? 'quay.io/pixelgen-technologies/pixelator:0.23.0'
         : 'quay.io/pixelgen-technologies/pixelator:0.23.0'}"
 
diff --git a/modules/local/pixelator/single-cell-pna/analysis/main.nf b/modules/local/pixelator/single-cell-pna/analysis/main.nf
@@ -5,7 +5,7 @@ process PIXELATOR_PNA_ANALYSIS {
     // TODO: Add conda
     // conda "bioconda::pixelator=0.18.2"
 
-    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+    container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
         ? 'quay.io/pixelgen-technologies/pixelator:0.23.0'
         : 'quay.io/pixelgen-technologies/pixelator:0.23.0'}"
 
diff --git a/modules/local/pixelator/single-cell-pna/collapse/main.nf b/modules/local/pixelator/single-cell-pna/collapse/main.nf
@@ -6,7 +6,7 @@ process PIXELATOR_PNA_COLLAPSE {
 
     // TODO: Add conda
     // conda "bioconda::pixelator=0.18.2"
-    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+    container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
         ? 'quay.io/pixelgen-technologies/pixelator:0.23.0'
         : 'quay.io/pixelgen-technologies/pixelator:0.23.0'}"
 
diff --git a/modules/local/pixelator/single-cell-pna/combine_collapse/main.nf b/modules/local/pixelator/single-cell-pna/combine_collapse/main.nf
@@ -5,7 +5,7 @@ process PIXELATOR_PNA_COMBINE_COLLAPSE {
     // TODO: Add conda
     // conda "bioconda::pixelator=0.18.2"
 
-    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+    container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
         ? 'quay.io/pixelgen-technologies/pixelator:0.23.0'
         : 'quay.io/pixelgen-technologies/pixelator:0.23.0'}"
 
diff --git a/modules/local/pixelator/single-cell-pna/demux/main.nf b/modules/local/pixelator/single-cell-pna/demux/main.nf
@@ -5,7 +5,7 @@ process PIXELATOR_PNA_DEMUX {
     // TODO: Add conda
     // conda "bioconda::pixelator=0.18.2"
 
-    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+    container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
         ? 'quay.io/pixelgen-technologies/pixelator:0.23.0'
         : 'quay.io/pixelgen-technologies/pixelator:0.23.0'}"
 
diff --git a/modules/local/pixelator/single-cell-pna/denoise/main.nf b/modules/local/pixelator/single-cell-pna/denoise/main.nf
@@ -5,7 +5,7 @@ process PIXELATOR_PNA_DENOISE {
     // TODO: Add conda
     // conda "bioconda::pixelator=0.18.2"
 
-    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+    container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
         ? 'quay.io/pixelgen-technologies/pixelator:0.23.0'
         : 'quay.io/pixelgen-technologies/pixelator:0.23.0'}"
 
diff --git a/modules/local/pixelator/single-cell-pna/graph/main.nf b/modules/local/pixelator/single-cell-pna/graph/main.nf
@@ -3,7 +3,7 @@ process PIXELATOR_PNA_GRAPH {
     label 'process_high_memory'
     label 'process_long'
 
-    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+    container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
         ? 'quay.io/pixelgen-technologies/pixelator:0.23.0'
         : 'quay.io/pixelgen-technologies/pixelator:0.23.0'}"
 
diff --git a/modules/local/pixelator/single-cell-pna/layout/main.nf b/modules/local/pixelator/single-cell-pna/layout/main.nf
@@ -4,7 +4,7 @@ process PIXELATOR_PNA_LAYOUT {
 
     // TODO: Add conda
     // conda "bioconda::pixelator=0.18.2"
-    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+    container "${params.pixelator_container?:workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
         ? 'quay.io/pixelgen-technologies/pixelator:0.23.0'
         : 'quay.io/pixelgen-technologies/pixelator:0.23.0'}"
 
diff --git a/nextflow.config b/nextflow.config
@@ -357,7 +357,7 @@ manifest {
     mainScript      = 'main.nf'
     defaultBranch   = 'master'
     nextflowVersion = '!>=25.04.0'
-    version         = '3.0.0'
+    version         = '3.0.1'
     doi             = '10.1101/2023.06.05.543770'
 }
 
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
diff --git a/tests/pna.nf.test.snap b/tests/pna.nf.test.snap
@@ -109,7 +109,7 @@
                     "pixelator": "0.23.0"
                 },
                 "Workflow": {
-                    "nf-core/pixelator": "v3.0.0"
+                    "nf-core/pixelator": "v3.0.1"
                 }
             }
         ],
@@ -154,7 +154,7 @@
                     "pixelator": "0.23.0"
                 },
                 "Workflow": {
-                    "nf-core/pixelator": "v3.0.0"
+                    "nf-core/pixelator": "v3.0.1"
                 }
             },
             [

Original file line number	Diff line number	Diff line change
`@@ -32,10 +32,6 @@ process {`
`32`	`32`	`pattern: '*.log'`
`33`	`33`	`]`
`34`	`34`	`]`
`35`		`-`
`36`		`- if (params.pixelator_container) {`
`37`		`- container = params.pixelator_container`
`38`		`- }`
`39`	`35`	`}`
`40`	`36`
`41`	`37`	`withName: PIXELATOR_LIST_OPTIONS {`
`@@ -45,10 +41,4 @@ process {`
`45`	`41`	`withName: "CAT_FASTQ" {`
`46`	`42`	`publishDir = [ enabled: false ]`
`47`	`43`	`}`
`48`		`-`
`49`		`- withName: "EXPERIMENT_SUMMARY" {`
`50`		`- if (params.experiment_summary_container) {`
`51`		`- container = params.experiment_summary_container`
`52`		`- }`
`53`		`- }`
`54`	`44`	`}`