update meta.yml plus snapshots

nf-core · Dec 10, 2024 · 2ab1ce0 · 2ab1ce0
1 parent 370c0dc
commit 2ab1ce0
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Showing 5 changed files with 25 additions and 46 deletions.
diff --git a/modules/nf-core/pangolin/run/meta.yml b/modules/nf-core/pangolin/run/meta.yml
@@ -4,6 +4,7 @@ keywords:
   - covid
   - pangolin
   - lineage
+  - run
 tools:
   - pangolin:
       description: |
@@ -21,6 +22,11 @@ input:
         type: file
         description: |
           The genome assembly to be evaluated
+  - - db:
+      type: directory
+      description: |
+        Directory containing the Pangolin database
+
 output:
   - report:
       - meta:

diff --git a/modules/nf-core/pangolin/updatedata/environment.yml b/modules/nf-core/pangolin/updatedata/environment.yml
@@ -1,7 +1,7 @@
----
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::pangolin=4.3.1"
+  - bioconda::pangolin-data=1.30
+  - bioconda::pangolin=4.3
+  - bioconda::snakemake=7.30.1
diff --git a/modules/nf-core/pangolin/updatedata/main.nf b/modules/nf-core/pangolin/updatedata/main.nf
@@ -4,8 +4,8 @@ process PANGOLIN_UPDATEDATA {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pangolin:4.3.1--pyhdfd78af_0':
-        'biocontainers/pangolin:4.3.1--pyhdfd78af_0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/bb/bb7bac48e43a9cd6274e1f99c761a5785b74f6d8a55313ee634aaffbe87c1869/data' :
+        'community.wave.seqera.io/library/pangolin-data_pangolin_snakemake:5bbc297f7502ff33' }"
 
     input:
     val(dbname)

diff --git a/modules/nf-core/pangolin/updatedata/meta.yml b/modules/nf-core/pangolin/updatedata/meta.yml
@@ -7,6 +7,7 @@ keywords:
   - pangolin
   - database
   - lineage
+  - updatedata
 tools:
   - pangolin:
       description: |
@@ -16,44 +17,16 @@ tools:
       licence: ["GPL-3.0-or-later"]
       identifier: biotools:pangolin_cov-lineages
 
-## TODO nf-core: Add a description of all of the variables used as input
 input:
-  # Only when we have meta
-  - - meta:
-        type: map
-        description: |
-          Groovy Map containing sample information
-          e.g. `[ id:'sample1', single_end:false ]`
-
-    ## TODO nf-core: Delete / customise this example input
-    - bam:
-        type: file
-        description: Sorted BAM/CRAM/SAM file
-        pattern: "*.{bam,cram,sam}"
-        ontologies:
-          - edam: "http://edamontology.org/format_25722"
-          - edam: "http://edamontology.org/format_2573"
-          - edam: "http://edamontology.org/format_3462"
-
-## TODO nf-core: Add a description of all of the variables used as output
+  - - dbname:
+        type: string
+        description: Name of directory to store the most recent pangolin dataset.
 output:
-  - bam:
-      #Only when we have meta
-      - meta:
-          type: map
-          description: |
-            Groovy Map containing sample information
-            e.g. `[ id:'sample1', single_end:false ]`
-      ## TODO nf-core: Delete / customise this example output
-      - "*.bam":
-          type: file
-          description: Sorted BAM/CRAM/SAM file
-          pattern: "*.{bam,cram,sam}"
-          ontologies:
-            - edam: "http://edamontology.org/format_25722"
-            - edam: "http://edamontology.org/format_2573"
-            - edam: "http://edamontology.org/format_3462"
-
+  - output:
+      - ${prefix}/:
+          type: directory
+          description: Directory containing downloaded data with directory naming being
+            the user provided dbname or prefix.
   - versions:
       - "versions.yml":
           type: file

diff --git a/modules/nf-core/pangolin/updatedata/tests/main.nf.test.snap b/modules/nf-core/pangolin/updatedata/tests/main.nf.test.snap
@@ -7,14 +7,14 @@
                 "pangolin_data-1.31.dist-info"
             ],
             [
-                "versions.yml:md5,1b004615fee194acc3bc79028c1ff8fc"
+                "versions.yml:md5,65119f93071bb8769953b7cb1aa9af4c"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2024-12-09T16:00:26.178983065"
+        "timestamp": "2024-12-10T10:18:37.005116436"
     },
     "str - testdb - stub": {
         "content": [
@@ -25,22 +25,22 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,1b004615fee194acc3bc79028c1ff8fc"
+                    "versions.yml:md5,65119f93071bb8769953b7cb1aa9af4c"
                 ],
                 "db": [
                     [
 
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,1b004615fee194acc3bc79028c1ff8fc"
+                    "versions.yml:md5,65119f93071bb8769953b7cb1aa9af4c"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2024-12-09T16:00:37.563640666"
+        "timestamp": "2024-12-10T10:20:56.504134367"
     }
 }