updated propr container

nf-core · Oct 18, 2024 · b566842 · b566842
1 parent 9819e84
commit b566842
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Showing 4 changed files with 10 additions and 13 deletions.
diff --git a/conf/test_experimental.config b/conf/test_experimental.config
@@ -29,7 +29,7 @@ params {
     input = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.samplesheet.csv'
     matrix =  'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv'
     contrasts =  'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.contrasts.csv'
-    pathway = "propd,propd_fdr,propr,cor"
+    pathway = "propd,propd_grea,propr,cor"
 
     //Features
     features_metadata_cols      = 'gene_id,gene_name'

diff --git a/modules/local/propr/grea/main.nf b/modules/local/propr/grea/main.nf
@@ -2,13 +2,10 @@ process PROPR_GREA {
     tag "$meta.id"
     label 'process_high'
 
-    // TODO
-    // the container is not updated for the grea function
-    // for the moment I'm running it locally
     // conda "${moduleDir}/environment.yml"
-    // container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-    //     'https://depot.galaxyproject.org/singularity/mulled-v2-401a215d4024df776a98d90a352048199e342a3d:5ba9bbf6cd4f4f98983526673c223d2e7d829b36-0':
-    //     'biocontainers/mulled-v2-401a215d4024df776a98d90a352048199e342a3d:5ba9bbf6cd4f4f98983526673c223d2e7d829b36-0' }"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'oras://community.wave.seqera.io/library/bioconductor-limma_r-ggplot2_r-propr:75e6dfd62a2313a9':
+        'community.wave.seqera.io/library/bioconductor-limma_r-ggplot2_r-propr:fbd569ab00953cb0' }"
 
     input:
     tuple val(meta), path(adj)

diff --git a/modules/local/propr/propd/main.nf b/modules/local/propr/propd/main.nf
@@ -2,10 +2,10 @@ process PROPR_PROPD {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "${moduleDir}/environment.yml"
+    // conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-401a215d4024df776a98d90a352048199e342a3d:5ba9bbf6cd4f4f98983526673c223d2e7d829b36-0':
-        'biocontainers/mulled-v2-401a215d4024df776a98d90a352048199e342a3d:5ba9bbf6cd4f4f98983526673c223d2e7d829b36-0' }"
+        'oras://community.wave.seqera.io/library/bioconductor-limma_r-ggplot2_r-propr:75e6dfd62a2313a9':
+        'community.wave.seqera.io/library/bioconductor-limma_r-ggplot2_r-propr:fbd569ab00953cb0' }"
 
     input:
     tuple val(meta), path(count), path(samplesheet), val(contrast_variable), val(reference), val(target)

diff --git a/modules/local/propr/propr/main.nf b/modules/local/propr/propr/main.nf
@@ -2,10 +2,10 @@ process PROPR_PROPR {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "${moduleDir}/environment.yml"
+    // conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-401a215d4024df776a98d90a352048199e342a3d:5ba9bbf6cd4f4f98983526673c223d2e7d829b36-0':
-        'biocontainers/mulled-v2-401a215d4024df776a98d90a352048199e342a3d:5ba9bbf6cd4f4f98983526673c223d2e7d829b36-0' }"
+        'oras://community.wave.seqera.io/library/bioconductor-limma_r-ggplot2_r-propr:75e6dfd62a2313a9':
+        'community.wave.seqera.io/library/bioconductor-limma_r-ggplot2_r-propr:fbd569ab00953cb0' }"
 
     input:
     tuple val(meta), path(count)