Merge pull request #115 from nf-core/update-containers

Update containers for 0.19.0
nf-core · Dec 11, 2024 · e1fd214 · e1fd214
2 parents 0777f78 + f6f937d
commit e1fd214
Show file tree

Hide file tree

Showing 18 changed files with 37 additions and 33 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[PR #112](https://github.com/nf-core/pixelator/pull/112)] - Add graph refinement options for pixelator 0.19
 - [[PR #113](https://github.com/nf-core/pixelator/pull/113)] - Fix validation issues after nf-core/tools v3.0.2 update
 - [[PR #114](https://github.com/nf-core/pixelator/pull/114)] - Remove `--save_recovered_components` options for graph outputs
+- [[PR #115](https://github.com/nf-core/pixelator/pull/115)] - Update containers for pixelator 0.19
 
 ### Parameters
 

diff --git a/conf/test_panel_v2.config b/conf/test_panel_v2.config
@@ -31,7 +31,7 @@ params {
     input_basedir  = params.pipelines_testdata_base_path + 'pixelator/testdata/'
 
     multiplet_recovery                = true
-    min_size                          = 2
+    min_size                          = 1
     max_size                          = 100000
     dynamic_filter                    = null
     compute_polarization              = true

diff --git a/modules.json b/modules.json
@@ -16,7 +16,7 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082",
+                        "git_sha": "c2b22d85f30a706a3073387f30380704fcae013b",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
@@ -26,7 +26,7 @@
                     },
                     "utils_nfschema_plugin": {
                         "branch": "master",
-                        "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c",
+                        "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e",
                         "installed_by": ["subworkflows"]
                     }
                 }

diff --git a/modules/local/pixelator/collect_metadata.nf b/modules/local/pixelator/collect_metadata.nf
@@ -8,8 +8,8 @@ process PIXELATOR_COLLECT_METADATA {
 
     conda "bioconda::pixelator=0.18.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pixelator:0.18.2--pyhdfd78af_0' :
-        'biocontainers/pixelator:0.18.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/pixelator:pixelator:0.19.0--pyhdfd78af_0' :
+        'biocontainers/pixelator:0.19.0--pyhdfd78af_0' }"
 
     input:
 

diff --git a/modules/local/pixelator/list_options.nf b/modules/local/pixelator/list_options.nf
@@ -4,8 +4,8 @@ process PIXELATOR_LIST_OPTIONS {
 
     conda "bioconda::pixelator=0.18.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pixelator:0.18.2--pyhdfd78af_0' :
-        'biocontainers/pixelator:0.18.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/pixelator:pixelator:0.19.0--pyhdfd78af_0' :
+        'biocontainers/pixelator:0.19.0--pyhdfd78af_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
@@ -5,8 +5,8 @@ process PIXELATOR_AMPLICON {
 
     conda "bioconda::pixelator=0.18.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pixelator:0.18.2--pyhdfd78af_0' :
-        'biocontainers/pixelator:0.18.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/pixelator:pixelator:0.19.0--pyhdfd78af_0' :
+        'biocontainers/pixelator:0.19.0--pyhdfd78af_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
@@ -4,8 +4,8 @@ process PIXELATOR_ANALYSIS {
 
     conda "bioconda::pixelator=0.18.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pixelator:0.18.2--pyhdfd78af_0' :
-        'biocontainers/pixelator:0.18.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/pixelator:pixelator:0.19.0--pyhdfd78af_0' :
+        'biocontainers/pixelator:0.19.0--pyhdfd78af_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
@@ -5,8 +5,8 @@ process PIXELATOR_ANNOTATE {
 
     conda "bioconda::pixelator=0.18.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pixelator:0.18.2--pyhdfd78af_0' :
-        'biocontainers/pixelator:0.18.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/pixelator:pixelator:0.19.0--pyhdfd78af_0' :
+        'biocontainers/pixelator:0.19.0--pyhdfd78af_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
@@ -4,8 +4,8 @@ process PIXELATOR_COLLAPSE {
 
     conda "bioconda::pixelator=0.18.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pixelator:0.18.2--pyhdfd78af_0' :
-        'biocontainers/pixelator:0.18.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/pixelator:pixelator:0.19.0--pyhdfd78af_0' :
+        'biocontainers/pixelator:0.19.0--pyhdfd78af_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
@@ -5,8 +5,8 @@ process PIXELATOR_DEMUX {
 
     conda "bioconda::pixelator=0.18.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pixelator:0.18.2--pyhdfd78af_0' :
-        'biocontainers/pixelator:0.18.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/pixelator:pixelator:0.19.0--pyhdfd78af_0' :
+        'biocontainers/pixelator:0.19.0--pyhdfd78af_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
@@ -5,8 +5,8 @@ process PIXELATOR_GRAPH {
 
     conda "bioconda::pixelator=0.18.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pixelator:0.18.2--pyhdfd78af_0' :
-        'biocontainers/pixelator:0.18.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/pixelator:pixelator:0.19.0--pyhdfd78af_0' :
+        'biocontainers/pixelator:0.19.0--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(edge_list)

diff --git a/modules/local/pixelator/single-cell/layout/main.nf b/modules/local/pixelator/single-cell/layout/main.nf
@@ -5,8 +5,8 @@ process PIXELATOR_LAYOUT {
 
     conda "bioconda::pixelator=0.18.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pixelator:0.18.2--pyhdfd78af_0' :
-        'biocontainers/pixelator:0.18.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/pixelator:pixelator:0.19.0--pyhdfd78af_0' :
+        'biocontainers/pixelator:0.19.0--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(data)

diff --git a/modules/local/pixelator/single-cell/qc/main.nf b/modules/local/pixelator/single-cell/qc/main.nf
@@ -5,8 +5,8 @@ process PIXELATOR_QC {
 
     conda "bioconda::pixelator=0.18.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pixelator:0.18.2--pyhdfd78af_0' :
-        'biocontainers/pixelator:0.18.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/pixelator:pixelator:0.19.0--pyhdfd78af_0' :
+        'biocontainers/pixelator:0.19.0--pyhdfd78af_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
@@ -5,8 +5,8 @@ process PIXELATOR_REPORT {
 
     conda "bioconda::pixelator=0.18.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pixelator:0.18.2--pyhdfd78af_0' :
-        'biocontainers/pixelator:0.18.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/pixelator:pixelator:0.19.0--pyhdfd78af_0' :
+        'biocontainers/pixelator:0.19.0--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(panel_file), val(panel)

diff --git a/nextflow.config b/nextflow.config
@@ -86,8 +86,7 @@ params {
     skip_layout                        = false
 
     // Main pixelator container override
-    // TODO: Remove this once the pixelator 0.19 is out
-    pixelator_container                = "ghcr.io/pixelgentechnologies/pixelator:dev"
+    pixelator_container                = null
 
     // Boilerplate options
     outdir                       = null

diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test