Merge pull request #6 from wsjung/update_containers

Update containers
wsjung · Feb 16, 2024 · 4c8047b · 4c8047b
2 parents 9fac026 + 98767aa
commit 4c8047b
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Showing 14 changed files with 42 additions and 12 deletions.
diff --git a/modules/local/cma/cma/main.nf b/modules/local/cma/cma/main.nf
@@ -2,7 +2,7 @@ process CMA {
 
     label 'process_low'
 
-    container 'docker://jungwooseok/cma:1.2.7' // TODO: replace when released on bioconductor
+    container 'jungwooseok/cma:1.2.7' // TODO: replace when released on bioconductor
 
     input:
     path input_files // list of input files to CMA (to accomodate arbitrary number of files)

diff --git a/modules/local/cma/format_cma_input/main.nf b/modules/local/cma/format_cma_input/main.nf
@@ -2,7 +2,6 @@ process FORMAT_CMA_INPUT {
 
     label 'process_medium'
 
-    // include an image docker/singularity from biocontainers
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/pandas:1.1.5' :

diff --git a/modules/local/mea/go_analysis/main.nf b/modules/local/mea/go_analysis/main.nf
@@ -2,7 +2,7 @@ process GO_ANALYSIS {
 
     label 'process_low'
 
-    container 'docker://jungwooseok/webgestalt:1.0.3'
+    container 'jungwooseok/webgestalt:1.0.3'
     // TODO: requested BioContainers
 
     input:

diff --git a/modules/local/mea/merge_ora_and_summary/environment.yml b/modules/local/mea/merge_ora_and_summary/environment.yml
@@ -0,0 +1,8 @@
+name: merge_ora_and_summary
+channels:
+    - conda-forge
+    - bioconda
+    - defaults
+dependencies:
+    - python=3.8.3
+    - pandas=1.1.5
diff --git a/modules/local/mea/merge_ora_and_summary/main.nf b/modules/local/mea/merge_ora_and_summary/main.nf
@@ -2,7 +2,7 @@ process MERGE_ORA_AND_SUMMARY {
 
     label 'process_low'
 
-    // container 'docker://jungwooseok/mea:1.0.0'
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/pandas:1.1.5' :
         'quay.io/biocontainers/pandas:1.1.5' }"

diff --git a/modules/local/mea/pascal/main.nf b/modules/local/mea/pascal/main.nf
@@ -2,7 +2,7 @@ process RUN_PASCAL {
 
     label 'process_low'
 
-    container 'docker://jungwooseok/mea_pascal:1.1'
+    container 'jungwooseok/mea_pascal:1.1'
 
     input:
     tuple val(module_id), path(geneScoreFile), path(moduleFile), path(goFile)

diff --git a/modules/local/mea/postprocess/environment.yml b/modules/local/mea/postprocess/environment.yml
@@ -0,0 +1,10 @@
+name: postprocess
+channels:
+    - conda-forge
+    - bioconda
+    - defaults
+dependencies:
+    - python=3.8.3
+    - pandas=2.2.0
+    - numpy=1.26.3
+    - statsmodels=0.14.1
diff --git a/modules/local/mea/postprocess/main.nf b/modules/local/mea/postprocess/main.nf
@@ -2,8 +2,13 @@ process POSTPROCESS_PASCAL {
 
     label 'process_low'
 
-    container 'docker://jungwooseok/mea:1.0.0'
+    // container 'jungwooseok/mea:1.0.0'
+    conda "${moduleDir}/environment.yml"
     // TODO: requested BioContainer
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mulled-v2-9d836da785124bb367cbe6fbfc00dddd2107a4da:b033d6a4ea3a42a6f5121a82b262800f1219b382-0' :
+        'quay.io/biocontainers/mulled-v2-9d836da785124bb367cbe6fbfc00dddd2107a4da:b033d6a4ea3a42a6f5121a82b262800f1219b382-0' }"
+
 
     input:
     tuple val(module_id), path(pascalOutputFile), path(geneScoreFilePascalInput), path(goFile)

diff --git a/modules/local/mea/preprocess/environment.yml b/modules/local/mea/preprocess/environment.yml
@@ -0,0 +1,8 @@
+name: merge_ora_and_summary
+channels:
+    - conda-forge
+    - bioconda
+    - defaults
+dependencies:
+    - python=3.8.3
+    - pandas=1.1.5
diff --git a/modules/local/mea/preprocess/main.nf b/modules/local/mea/preprocess/main.nf
@@ -2,7 +2,7 @@ process PREPROCESS_PASCAL {
 
     label 'process_low'
 
-    // container 'docker://jungwooseok/mea:1.0.0'
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/pandas:1.1.5' :
         'quay.io/biocontainers/pandas:1.1.5' }"

diff --git a/modules/local/mmap/mmap/main.nf b/modules/local/mmap/mmap/main.nf
@@ -2,7 +2,7 @@ process MMAP {
 
     label 'process_low'
 
-    container 'docker://jungwooseok/mmap:1.0.2'
+    container 'jungwooseok/mmap:1.0.2'
 
     input:
     val gene

diff --git a/modules/local/mmap/mmap_parse/main.nf b/modules/local/mmap/mmap_parse/main.nf
@@ -5,7 +5,7 @@ process MMAP_PARSE {
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-344874846f44224e5f0b7b741eacdddffe895d1e:d3fff24ee1297b4c3bcef48354c2a30f0c82007a-0' :
-        'biocontainers/mulled-v2-344874846f44224e5f0b7b741eacdddffe895d1e:d3fff24ee1297b4c3bcef48354c2a30f0c82007a-0' }"
+        'quay.io/biocontainers/mulled-v2-344874846f44224e5f0b7b741eacdddffe895d1e:d3fff24ee1297b4c3bcef48354c2a30f0c82007a-0' }"
 
     input:
     path output_MMAP

diff --git a/modules/local/pascal/main.nf b/modules/local/pascal/main.nf
@@ -1,7 +1,7 @@
 process PASCAL {
     label 'process_medium'
 
-    container 'docker://jungwooseok/pascal:1.0.3'
+    container 'jungwooseok/pascal:1.0.3'
 
     // publishDir "results/pascal", mode:'copy', saveAs: { filename  -> filename.endsWith(".csv") ? "PASCAL.csv" : filename}
 

diff --git a/nextflow.config b/nextflow.config
@@ -170,9 +170,9 @@ profiles {
 // Will not be used unless Apptainer / Docker / Podman / Singularity are enabled
 // Set to your registry if you have a mirror of containers
 apptainer.registry   = 'quay.io'
-docker.registry      = 'quay.io'
+docker.registry      = 'docker.io'
 podman.registry      = 'quay.io'
-singularity.registry = 'quay.io'
+singularity.registry = 'docker.io'
 
 // Nextflow plugins
 plugins {