update crabs with wave containers

nf-core · Sep 5, 2024 · eec926c · eec926c
1 parent 115f539
commit eec926c
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Showing 3 changed files with 16 additions and 14 deletions.
diff --git a/modules/nf-core/crabs/dbimport/environment.yml b/modules/nf-core/crabs/dbimport/environment.yml
@@ -3,4 +3,9 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::crabs=0.1.1"
+  - wget=1.21.3
+  - muscle=3.8.31
+  - cutadapt>=4.0
+  - vsearch>=2.13.3
+  - pip:
+      - crabs==0.2
diff --git a/modules/nf-core/crabs/dbimport/main.nf b/modules/nf-core/crabs/dbimport/main.nf
@@ -2,11 +2,10 @@ process CRABS_DBIMPORT {
     tag "$meta.id"
     label 'process_medium'
 
-    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/crabs:0.1.1--pyhb7b1952_0':
-        'biocontainers/crabs:0.1.1--pyhb7b1952_0' }"
+        'oras://community.wave.seqera.io/library/cutadapt_muscle_vsearch_wget_pruned:0cd5cb1e549e5033':
+        'community.wave.seqera.io/library/cutadapt_muscle_vsearch_wget_pruned:04f6c0370c0226c5' }"
 
     input:
     tuple val(meta), path(fasta)
@@ -21,7 +20,6 @@ process CRABS_DBIMPORT {
     script:
     def args          = task.ext.args ?: ''
     def prefix        = task.ext.prefix ?: "${meta.id}"
-    def VERSION       = '0.1.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     def is_compressed = fasta.name.endsWith(".gz")
     def fasta_name    = fasta.name.replace(".gz", "")
     """
@@ -38,19 +36,18 @@ process CRABS_DBIMPORT {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        crabs: $VERSION
+        crabs: \$(crabs --version | sed -e 's/crabs v//g')
     END_VERSIONS
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def VERSION       = '0.1.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     touch ${prefix}.fa
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        crabs: $VERSION
+        crabs: \$(crabs --version | sed -e 's/crabs v//g')
     END_VERSIONS
     """
 }
diff --git a/modules/nf-core/crabs/dbimport/tests/main.nf.test.snap b/modules/nf-core/crabs/dbimport/tests/main.nf.test.snap
@@ -11,7 +11,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,aa9d175ec56d1dce0a3588883ab1b00a"
+                    "versions.yml:md5,4f1f73cb937227ccf6abfa3002824535"
                 ],
                 "fasta": [
                     [
@@ -22,15 +22,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,aa9d175ec56d1dce0a3588883ab1b00a"
+                    "versions.yml:md5,4f1f73cb937227ccf6abfa3002824535"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-05T12:42:46.076137"
+        "timestamp": "2024-09-05T15:25:04.701271"
     },
     "sarscov2 - fasta": {
         "content": [
@@ -44,7 +44,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,aa9d175ec56d1dce0a3588883ab1b00a"
+                    "versions.yml:md5,4f1f73cb937227ccf6abfa3002824535"
                 ],
                 "fasta": [
                     [
@@ -55,14 +55,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,aa9d175ec56d1dce0a3588883ab1b00a"
+                    "versions.yml:md5,4f1f73cb937227ccf6abfa3002824535"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-05T12:42:41.421262"
+        "timestamp": "2024-09-05T15:24:57.657881"
     }
 }