add native singularity image for pixelator

nf-core · Oct 17, 2023 · 6bf0935 · 6bf0935
1 parent 08d5be6
commit 6bf0935
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Showing 10 changed files with 30 additions and 10 deletions.
diff --git a/modules/local/pixelator/collect_metadata.nf b/modules/local/pixelator/collect_metadata.nf
@@ -9,7 +9,9 @@ process PIXELATOR_COLLECT_METADATA {
     cache false
 
     conda "bioconda::pixelator=0.15.0"
-    container "biocontainers/pixelator:0.15.0--pyh7cba7a3_0"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/pixelator:0.15.0--pyh7cba7a3_0' :
+        'biocontainers/pixelator:0.15.0--pyh7cba7a3_0' }"
 
     input:
 

diff --git a/modules/local/pixelator/list_options.nf b/modules/local/pixelator/list_options.nf
@@ -3,7 +3,9 @@ process PIXELATOR_LIST_OPTIONS {
 
 
     conda "bioconda::pixelator=0.15.0"
-    container "biocontainers/pixelator:0.15.0--pyh7cba7a3_0"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/pixelator:0.15.0--pyh7cba7a3_0' :
+        'biocontainers/pixelator:0.15.0--pyh7cba7a3_0' }"
 
     output:
     path "design_options.txt"     , emit: designs

diff --git a/modules/local/pixelator/single-cell/amplicon/main.nf b/modules/local/pixelator/single-cell/amplicon/main.nf
@@ -4,7 +4,9 @@ process PIXELATOR_AMPLICON {
 
 
     conda "bioconda::pixelator=0.15.0"
-    container "biocontainers/pixelator:0.15.0--pyh7cba7a3_0"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/pixelator:0.15.0--pyh7cba7a3_0' :
+        'biocontainers/pixelator:0.15.0--pyh7cba7a3_0' }"
 
     input:
     tuple val(meta), path(reads)

diff --git a/modules/local/pixelator/single-cell/analysis/main.nf b/modules/local/pixelator/single-cell/analysis/main.nf
@@ -4,7 +4,9 @@ process PIXELATOR_ANALYSIS {
 
 
     conda "bioconda::pixelator=0.15.0"
-    container "biocontainers/pixelator:0.15.0--pyh7cba7a3_0"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/pixelator:0.15.0--pyh7cba7a3_0' :
+        'biocontainers/pixelator:0.15.0--pyh7cba7a3_0' }"
 
     input:
     tuple val(meta), path(data)

diff --git a/modules/local/pixelator/single-cell/annotate/main.nf b/modules/local/pixelator/single-cell/annotate/main.nf
@@ -4,7 +4,9 @@ process PIXELATOR_ANNOTATE {
 
 
     conda "bioconda::pixelator=0.15.0"
-    container "biocontainers/pixelator:0.15.0--pyh7cba7a3_0"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/pixelator:0.15.0--pyh7cba7a3_0' :
+        'biocontainers/pixelator:0.15.0--pyh7cba7a3_0' }"
 
     input:
     tuple val(meta), path(dataset), path(panel_file), val(panel)

diff --git a/modules/local/pixelator/single-cell/collapse/main.nf b/modules/local/pixelator/single-cell/collapse/main.nf
@@ -3,7 +3,9 @@ process PIXELATOR_COLLAPSE {
     label 'process_medium'
 
     conda "bioconda::pixelator=0.15.0"
-    container "biocontainers/pixelator:0.15.0--pyh7cba7a3_0"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/pixelator:0.15.0--pyh7cba7a3_0' :
+        'biocontainers/pixelator:0.15.0--pyh7cba7a3_0' }"
 
     input:
     tuple val(meta), path(reads), path(panel_file), val(panel)

diff --git a/modules/local/pixelator/single-cell/demux/main.nf b/modules/local/pixelator/single-cell/demux/main.nf
@@ -4,7 +4,9 @@ process PIXELATOR_DEMUX {
 
 
     conda "bioconda::pixelator=0.15.0"
-    container "biocontainers/pixelator:0.15.0--pyh7cba7a3_0"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/pixelator:0.15.0--pyh7cba7a3_0' :
+        'biocontainers/pixelator:0.15.0--pyh7cba7a3_0' }"
 
     input:
     tuple val(meta), path(reads), path(panel_file), val(panel)

diff --git a/modules/local/pixelator/single-cell/graph/main.nf b/modules/local/pixelator/single-cell/graph/main.nf
@@ -4,7 +4,9 @@ process PIXELATOR_GRAPH {
 
 
     conda "bioconda::pixelator=0.15.0"
-    container "biocontainers/pixelator:0.15.0--pyh7cba7a3_0"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/pixelator:0.15.0--pyh7cba7a3_0' :
+        'biocontainers/pixelator:0.15.0--pyh7cba7a3_0' }"
 
     input:
     tuple val(meta), path(edge_list)

diff --git a/modules/local/pixelator/single-cell/qc/main.nf b/modules/local/pixelator/single-cell/qc/main.nf
@@ -4,7 +4,9 @@ process PIXELATOR_QC {
 
 
     conda "bioconda::pixelator=0.15.0"
-    container "biocontainers/pixelator:0.15.0--pyh7cba7a3_0"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/pixelator:0.15.0--pyh7cba7a3_0' :
+        'biocontainers/pixelator:0.15.0--pyh7cba7a3_0' }"
 
     input:
     tuple val(meta), path(reads)

diff --git a/modules/local/pixelator/single-cell/report/main.nf b/modules/local/pixelator/single-cell/report/main.nf
@@ -4,7 +4,9 @@ process PIXELATOR_REPORT {
 
 
     conda "bioconda::pixelator=0.15.0"
-    container "biocontainers/pixelator:0.15.0--pyh7cba7a3_0"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/pixelator:0.15.0--pyh7cba7a3_0' :
+        'biocontainers/pixelator:0.15.0--pyh7cba7a3_0' }"
 
     input:
     tuple val(meta), path(panel_file), val(panel)