Unify container definitions

Mye-InfoBank · Apr 9, 2024 · d758e59 · d758e59
1 parent 0c7ceb5
commit d758e59
Showing 30 changed files with 33 additions and 33 deletions.
diff --git a/modules/cell_cycle.nf b/modules/cell_cycle.nf
@@ -5,7 +5,7 @@ process CELL_CYCLE {
     label "process_high_memory"
     errorStrategy 'retry'
 
-    container = "bigdatainbiomedicine/sc-scib:1.0"
+    container = "bigdatainbiomedicine/sc-scib:1.2"
 
     input:
         tuple val(meta), path(adata)

diff --git a/modules/cell_qc.nf b/modules/cell_qc.nf
@@ -1,6 +1,6 @@
 process CELL_QC {
   tag "$meta.id"
-  container "bigdatainbiomedicine/sc-rpy:1.0"
+  container "bigdatainbiomedicine/sc-rpy:1.2"
 
   label "process_medium"
 

diff --git a/modules/celltypist.nf b/modules/celltypist.nf
@@ -1,7 +1,7 @@
 process CELLTYPIST {
     tag "$meta.id"
 
-    container "bigdatainbiomedicine/sc-rpy:1.0"
+    container "bigdatainbiomedicine/sc-rpy:1.2"
 
     label "process_high"
     label "process_high_memory"
@@ -25,7 +25,7 @@ process CELLTYPIST {
 process CELLTYPIST_MAJORITY {
     tag "${meta.id}"
 
-    container "bigdatainbiomedicine/sc-rpy:1.0"
+    container "bigdatainbiomedicine/sc-rpy:1.2"
     label "process_medium"
 
     input:

diff --git a/modules/clean_adata.nf b/modules/clean_adata.nf
@@ -1,6 +1,6 @@
 process CLEAN_ADATA {
   tag "${meta.id}"
-  container "bigdatainbiomedicine/sc-rpy:1.0"
+  container "bigdatainbiomedicine/sc-rpy:1.2"
 
   label "process_high_memory"
 

diff --git a/modules/collect_problems.nf b/modules/collect_problems.nf
@@ -1,5 +1,5 @@
 process COLLECT_PROBLEMS {
-  container "bigdatainbiomedicine/sc-rpy:1.0"
+  container "bigdatainbiomedicine/sc-rpy:1.2"
 
   publishDir "${params.outdir}", mode: "${params.publish_mode}"
 

diff --git a/modules/composition.nf b/modules/composition.nf
@@ -1,5 +1,5 @@
 process COMPOSITION {
-    container "bigdatainbiomedicine/sc-rpy:1.0"
+    container "bigdatainbiomedicine/sc-rpy:1.2"
 
     publishDir "${params.outdir}/composition", mode: "${params.publish_mode}"
 

diff --git a/modules/decontX.nf b/modules/decontX.nf
@@ -1,7 +1,7 @@
 process DECONTX {
   tag "$meta.id"
 
-  container "bigdatainbiomedicine/sc-rpy:1.0"
+  container "bigdatainbiomedicine/sc-rpy:1.2"
 
   label "process_medium"
   label "process_high_memory"

diff --git a/modules/dedoublet_adata.nf b/modules/dedoublet_adata.nf
@@ -1,6 +1,6 @@
 process DEDOUBLET_ADATA {
     tag "${meta.id}"
-    container "bigdatainbiomedicine/sc-rpy:1.0"
+    container "bigdatainbiomedicine/sc-rpy:1.2"
 
     label "process_medium"
 

diff --git a/modules/distribution.nf b/modules/distribution.nf
@@ -1,5 +1,5 @@
 process DISTRIBUTION {
-    container "bigdatainbiomedicine/sc-rpy:1.0"
+    container "bigdatainbiomedicine/sc-rpy:1.2"
 
     publishDir "${params.outdir}/distribution", mode: "${params.publish_mode}"
 

diff --git a/modules/entropy.nf b/modules/entropy.nf
@@ -1,7 +1,7 @@
 process ENTROPY {
   tag "${meta.id}"
 
-  container "bigdatainbiomedicine/sc-rpy:1.0"
+  container "bigdatainbiomedicine/sc-rpy:1.2"
   label "process_medium"
   errorStrategy { task.attempt < 7 ? 'retry' : 'ignore'}
 

diff --git a/modules/extract_embedding.nf b/modules/extract_embedding.nf
@@ -1,6 +1,6 @@
 process EXTRACT_EMBEDDING {
   tag "${meta.id}"
-  container "bigdatainbiomedicine/sc-rpy:1.0"
+  container "bigdatainbiomedicine/sc-rpy:1.2"
 
   label "process_medium"
 

diff --git a/modules/genes_upset.nf b/modules/genes_upset.nf
@@ -1,5 +1,5 @@
 process GENES_UPSET {
-    container "bigdatainbiomedicine/sc-rpy:1.1"
+    container "bigdatainbiomedicine/sc-rpy:1.2"
 
     publishDir "${params.outdir}", mode: "${params.publish_mode}"
 

diff --git a/modules/get_batches.nf b/modules/get_batches.nf
@@ -1,7 +1,7 @@
 process GET_BATCHES {
     tag "$meta.id"
 
-    container "bigdatainbiomedicine/sc-rpy:1.0"
+    container "bigdatainbiomedicine/sc-rpy:1.2"
 
     label "process_medium"
 

diff --git a/modules/identify_hvgs.nf b/modules/identify_hvgs.nf
@@ -1,7 +1,7 @@
 process IDENTIFY_HVGS {
     tag "$meta.id"
 
-    container "bigdatainbiomedicine/sc-rpy:1.0"
+    container "bigdatainbiomedicine/sc-rpy:1.2"
 
     label "process_medium"
 

diff --git a/modules/integrate.nf b/modules/integrate.nf
@@ -1,6 +1,6 @@
 process INTEGRATE {
   tag "${method}"
-  container "bigdatainbiomedicine/sc-scib:1.0"
+  container "bigdatainbiomedicine/sc-scib:1.2"
 
   label "process_high"
 

diff --git a/modules/leiden.nf b/modules/leiden.nf
@@ -1,7 +1,7 @@
 process LEIDEN {
     tag "${meta.id}:${resolution}"
 
-    container = "bigdatainbiomedicine/sc-rpy:1.0"
+    container = "bigdatainbiomedicine/sc-rpy:1.2"
     label "process_medium"
 
     input:

diff --git a/modules/merge.nf b/modules/merge.nf
@@ -1,6 +1,6 @@
 process MERGE {
   tag "${meta.id}"
-  container "bigdatainbiomedicine/sc-rpy:1.0"
+  container "bigdatainbiomedicine/sc-rpy:1.2"
 
   publishDir "${params.outdir}", mode: "${params.publish_mode}"
 

diff --git a/modules/merge_clustering.nf b/modules/merge_clustering.nf
@@ -1,7 +1,7 @@
 process MERGE_CLUSTERING {
     tag "${meta.id}"
 
-    container = "bigdatainbiomedicine/sc-rpy:1.0"
+    container = "bigdatainbiomedicine/sc-rpy:1.2"
     label "process_medium"
 
 

diff --git a/modules/merge_datasets.nf b/modules/merge_datasets.nf
@@ -1,5 +1,5 @@
 process MERGE_DATASETS {
-  container "bigdatainbiomedicine/sc-rpy:1.0"
+  container "bigdatainbiomedicine/sc-rpy:1.2"
 
   label "process_medium"
 

diff --git a/modules/merge_extended.nf b/modules/merge_extended.nf
@@ -1,7 +1,7 @@
 process MERGE_EXTENDED {
     tag "${meta.id}"
 
-    container "bigdatainbiomedicine/sc-rpy:1.0"
+    container "bigdatainbiomedicine/sc-rpy:1.2"
 
     label "process_medium"
 

diff --git a/modules/neighbors.nf b/modules/neighbors.nf
@@ -1,7 +1,7 @@
 process NEIGHBORS {
     tag "${meta.id}"
 
-    container = "bigdatainbiomedicine/sc-rpy:1.0"
+    container = "bigdatainbiomedicine/sc-rpy:1.2"
     label "process_medium"
 
     input:

diff --git a/modules/normalize.nf b/modules/normalize.nf
@@ -2,7 +2,7 @@
 process NORMALIZE {
     tag "${meta.id}"
 
-    container = "bigdatainbiomedicine/sc-rpy:1.0"
+    container = "bigdatainbiomedicine/sc-rpy:1.2"
     label "process_high"
     label "process_high_memory"
 

diff --git a/modules/rds_to_h5ad.nf b/modules/rds_to_h5ad.nf
@@ -1,7 +1,7 @@
 process RDS_TO_H5AD {
   tag "${meta.id}"
 
-  container "bigdatainbiomedicine/sc-rpy:1.0"
+  container "bigdatainbiomedicine/sc-rpy:1.2"
   label "process_medium"
 
   input:

diff --git a/modules/rename_integrations.nf b/modules/rename_integrations.nf
@@ -1,6 +1,6 @@
 process RENAME_INTEGRATIONS {
   tag "${meta.id}"
-  container "bigdatainbiomedicine/sc-rpy:1.0"
+  container "bigdatainbiomedicine/sc-rpy:1.2"
 
   publishDir "${params.outdir}", mode: "${params.publish_mode}"
 

diff --git a/modules/scIB.nf b/modules/scIB.nf
@@ -3,7 +3,7 @@ process BENCHMARK_INTEGRATIONS {
 
     label "process_high"
 
-    container = "bigdatainbiomedicine/sc-scib:1.0"
+    container = "bigdatainbiomedicine/sc-scib:1.2"
 
     input: 
         tuple val(meta1), path(uncorrected)
@@ -29,7 +29,7 @@ process MERGE_BENCHMARKS {
 
     publishDir "${params.outdir}", mode: "${params.publish_mode}"
 
-    container = "bigdatainbiomedicine/sc-rpy:1.0"
+    container = "bigdatainbiomedicine/sc-rpy:1.2"
 
     input:
         path(benchmarks)

diff --git a/modules/sc_SHC.nf b/modules/sc_SHC.nf
@@ -1,7 +1,7 @@
 process SCSHC_CLUSTERING {
     tag "${meta.id}"
 
-    container = "bigdatainbiomedicine/sc-rpy:1.1"
+    container = "bigdatainbiomedicine/sc-rpy:1.2"
     label "process_high"
 
     input:
@@ -44,7 +44,7 @@ process SCSHC_CLUSTERING {
 process SCSHC_CLUSTERING_QC {
     tag "${meta.id}"
 
-    container = "bigdatainbiomedicine/sc-rpy:1.1"
+    container = "bigdatainbiomedicine/sc-rpy:1.2"
     publishDir "${params.outdir}/clustering_qc", mode: "${params.publish_mode}", pattern: "*.png"
     label "process_high"
 

diff --git a/modules/solo.nf b/modules/solo.nf
@@ -1,6 +1,6 @@
 process SOLO {
     tag "${meta.id}"
-    container "bigdatainbiomedicine/sc-scib:1.0"
+    container "bigdatainbiomedicine/sc-scib:1.2"
 
     label "process_medium"
     label "process_high_memory"

diff --git a/modules/split_categories.nf b/modules/split_categories.nf
@@ -1,7 +1,7 @@
 process SPLIT_CATEGORIES {
     tag "$meta.id"
 
-    container "bigdatainbiomedicine/sc-rpy:1.0"
+    container "bigdatainbiomedicine/sc-rpy:1.2"
 
     label "process_medium"
 

diff --git a/modules/stop_if_problems.nf b/modules/stop_if_problems.nf
@@ -1,5 +1,5 @@
 process STOP_IF_PROBLEMS {
-  container "bigdatainbiomedicine/sc-rpy:1.0"
+  container "bigdatainbiomedicine/sc-rpy:1.2"
 
   label "process_single"
 

diff --git a/modules/umap.nf b/modules/umap.nf
@@ -1,7 +1,7 @@
 process UMAP {
     tag "${meta.id}"
 
-    container = "bigdatainbiomedicine/sc-rpy:1.0"
+    container = "bigdatainbiomedicine/sc-rpy:1.2"
     label "process_medium"
 
     input: