pangolin - use seqera containers + nf-test; rm pytests (#6740)

* use seqera containers + nf-test; rm pytests * Update modules/nf-core/pangolin/main.nf Co-authored-by: Joon Klaps <[email protected]> * update snapshots * fix home path sing & update conda env * Fixing the meta.yml and pining pangolin-data --------- Co-authored-by: Joon Klaps <[email protected]>
nf-core · Oct 18, 2024 · 9530ba6 · 9530ba6
1 parent a591752
commit 9530ba6
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Showing 9 changed files with 136 additions and 34 deletions.
diff --git a/modules/nf-core/pangolin/environment.yml b/modules/nf-core/pangolin/environment.yml
@@ -2,4 +2,6 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::pangolin=4.2
+  - bioconda::pangolin-data=1.30
+  - bioconda::pangolin=4.3
+  - bioconda::snakemake=7.30.1
diff --git a/modules/nf-core/pangolin/main.nf b/modules/nf-core/pangolin/main.nf
@@ -4,8 +4,8 @@ process PANGOLIN {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pangolin:4.2--pyhdfd78af_1' :
-        'biocontainers/pangolin:4.2--pyhdfd78af_1' }"
+        '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:
     tuple val(meta), path(fasta)
@@ -21,6 +21,8 @@ process PANGOLIN {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
+    export XDG_CACHE_HOME=/tmp/.cache
+
     pangolin \\
         $fasta\\
         --outfile ${prefix}.pangolin.csv \\

diff --git a/modules/nf-core/pangolin/meta.yml b/modules/nf-core/pangolin/meta.yml
@@ -5,7 +5,7 @@ keywords:
   - pangolin
   - lineage
 tools:
-  - star:
+  - pangolin:
       description: |
         Phylogenetic Assignment of Named Global Outbreak LINeages
       homepage: https://github.com/cov-lineages/pangolin#pangolearn-description
@@ -24,9 +24,9 @@ input:
 output:
   - report:
       - meta:
-          type: file
-          description: Pangolin lineage report
-          pattern: "*.{csv}"
+          type: map
+          description: |
+            Groovy Map containing sample information
       - "*.csv":
           type: file
           description: Pangolin lineage report

diff --git a/modules/nf-core/pangolin/tests/main.nf.test b/modules/nf-core/pangolin/tests/main.nf.test
@@ -0,0 +1,57 @@
+nextflow_process {
+
+    name "Test Process PANGOLIN"
+    script "../main.nf"
+    process "PANGOLIN"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "pangolin"
+
+    test("sarscov2 genome [fasta]") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                            [ id:'test' ], // meta map
+                            [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 genome [fasta] - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                            [ id:'test' ], // meta map
+                            [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/pangolin/tests/main.nf.test.snap b/modules/nf-core/pangolin/tests/main.nf.test.snap
@@ -0,0 +1,68 @@
+{
+    "sarscov2 genome [fasta] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.pangolin.csv:md5,2cc701567cf37bad5c6574c29aa595d4"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,65ec45a19faa92a922073b9b08d90a8a"
+                ],
+                "report": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.pangolin.csv:md5,2cc701567cf37bad5c6574c29aa595d4"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,65ec45a19faa92a922073b9b08d90a8a"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-18T10:33:48.797026222"
+    },
+    "sarscov2 genome [fasta]": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.pangolin.csv:md5,2cc701567cf37bad5c6574c29aa595d4"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,65ec45a19faa92a922073b9b08d90a8a"
+                ],
+                "report": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.pangolin.csv:md5,2cc701567cf37bad5c6574c29aa595d4"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,65ec45a19faa92a922073b9b08d90a8a"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-18T10:33:17.535254436"
+    }
+}
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -476,9 +476,6 @@ nucmer:
 oncocnv:
   - modules/nf-core/oncocnv/**
   - tests/modules/nf-core/oncocnv/**
-pangolin:
-  - modules/nf-core/pangolin/**
-  - tests/modules/nf-core/pangolin/**
 parabricks/applybqsr:
   - modules/nf-core/parabricks/applybqsr/**
   - tests/modules/nf-core/parabricks/applybqsr/**

diff --git a/tests/modules/nf-core/pangolin/main.nf b/tests/modules/nf-core/pangolin/main.nf
diff --git a/tests/modules/nf-core/pangolin/nextflow.config b/tests/modules/nf-core/pangolin/nextflow.config
diff --git a/tests/modules/nf-core/pangolin/test.yml b/tests/modules/nf-core/pangolin/test.yml