Update CADD to version 1.6.post1 and include Smk environments in cont…

…ainers (#4610) * New CADD version + new container images * enable new cadd release from conda * Force the registry to Docker Hub Registry quay.io is the default and it only contains packages built directly from conda * Make the license string into an array, as required by lint * Fix conda dependencies * Revert changes to mamba and conda version- keep as before --------- Co-authored-by: Marius Bjørnstad <[email protected]> Co-authored-by: Simon Pearce <[email protected]>
nf-core · May 15, 2024 · 35a1935 · 35a1935
1 parent cee8fe3
commit 35a1935
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Showing 3 changed files with 8 additions and 9 deletions.
diff --git a/modules/nf-core/cadd/environment.yml b/modules/nf-core/cadd/environment.yml
@@ -4,6 +4,6 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::cadd-scripts=1.6
+  - bioconda::cadd-scripts=1.6.post1
   - anaconda::conda=4.14.0
   - conda-forge::mamba=1.4.0
diff --git a/modules/nf-core/cadd/main.nf b/modules/nf-core/cadd/main.nf
@@ -3,14 +3,12 @@ process CADD {
     label 'process_medium'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-8d145e7b16a8ca4bf920e6ca464763df6f0a56a2:d4e457a2edecb2b10e915c01d8f46e29e236b648-0':
-        'biocontainers/mulled-v2-8d145e7b16a8ca4bf920e6ca464763df6f0a56a2:d4e457a2edecb2b10e915c01d8f46e29e236b648-0' }"
+    container 'docker.io/biocontainers/cadd-scripts-with-envs:1.6.post1_cv1'
 
     containerOptions {
         (workflow.containerEngine == 'singularity') ?
-            "--writable -B ${annotation_dir}:/usr/local/share/cadd-scripts-1.6-1/data/annotations" :
-            "--privileged -v ${annotation_dir}:/usr/local/share/cadd-scripts-1.6-1/data/annotations"
+            "-B ${annotation_dir}:/opt/CADD-scripts-1.6.post1/data/annotations" :
+            "-v ${annotation_dir}:/opt/CADD-scripts-1.6.post1/data/annotations"
         }
 
     input:
@@ -27,7 +25,7 @@ process CADD {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def VERSION = "1.6" // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
+    def VERSION = "1.6.post1" // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     """
     cadd.sh \\
         -o ${prefix}.tsv.gz \\
@@ -43,7 +41,7 @@ process CADD {
     stub:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def VERSION = "1.6" // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
+    def VERSION = "1.6.post1" // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     """
     touch ${prefix}.tsv.gz
 

diff --git a/modules/nf-core/cadd/meta.yml b/modules/nf-core/cadd/meta.yml
@@ -11,7 +11,8 @@ tools:
       documentation: "https://github.com/kircherlab/CADD-scripts/blob/master/README.md"
       tool_dev_url: "https://github.com/kircherlab/CADD-scripts/"
       doi: "10.1093/nar/gky1016"
-      licence: "['Restricted. Free for non-commercial users.']"
+      licence:
+        - Restricted. Free for non-commercial users.
 input:
   - meta:
       type: map