Update Abricate to include (missing) additional optional input channe…

…l and add stub (nf-core#5849) * Add missing optional input channel to abricate * Update abricate module to include missing optional input path * Update modules/nf-core/abricate/run/tests/main.nf.test Co-authored-by: Carson J Miller <[email protected]> * Fix linting * Update modules/nf-core/abricate/run/main.nf * Get downstream module test --------- Co-authored-by: Carson J Miller <[email protected]>
asp8200 · Jun 19, 2024 · d19df06 · d19df06
1 parent be84844
commit d19df06
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Showing 5 changed files with 94 additions and 4 deletions.
diff --git a/modules/nf-core/abricate/run/main.nf b/modules/nf-core/abricate/run/main.nf
@@ -9,6 +9,7 @@ process ABRICATE_RUN {
 
     input:
     tuple val(meta), path(assembly)
+    path databasedir
 
     output:
     tuple val(meta), path("*.txt"), emit: report
@@ -20,11 +21,27 @@ process ABRICATE_RUN {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def datadir = databasedir ? "--datadir ${databasedir}" : ''
     """
     abricate \\
         $assembly \\
         $args \\
-        --threads $task.cpus > ${prefix}.txt
+        $datadir \\
+        --threads $task.cpus \\
+        > ${prefix}.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        abricate: \$(echo \$(abricate --version 2>&1) | sed 's/^.*abricate //' )
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def datadir = databasedir ? '--datadir ${databasedir}' : ''
+    """
+    touch ${prefix}.txt
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/nf-core/abricate/run/meta.yml b/modules/nf-core/abricate/run/meta.yml
@@ -21,6 +21,10 @@ input:
       type: file
       description: FASTA, GenBank or EMBL formatted file
       pattern: "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz,gbk,gbk.gz,embl,embl.gz}"
+  - databasedir:
+      type: directory
+      description: Optional location of local copy of database files, possibly with custom databases set up with `abricate --setupdb`
+      pattern: "*/"
 output:
   - meta:
       type: map

diff --git a/modules/nf-core/abricate/run/tests/main.nf.test b/modules/nf-core/abricate/run/tests/main.nf.test
@@ -8,7 +8,7 @@ nextflow_process {
     tag "abricate"
     tag "abricate/run"
 
-    test("Should run without failures") {
+    test("bacteroides_fragilis - genome.fa.gz") {
 
         when {
             params {
@@ -20,6 +20,34 @@ nextflow_process {
                                 [ id:'test', single_end:false ], // meta map
                                 file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)
                             ]
+                input[1] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+            { assert process.success },
+            { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("bacteroides_fragilis - genome - stub") {
+
+        options "-stub"
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = [
+                                [ id:'test', single_end:false ], // meta map
+                                file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)
+                            ]
+                input[1] = []
                 """
             }
         }

diff --git a/modules/nf-core/abricate/run/tests/main.nf.test.snap b/modules/nf-core/abricate/run/tests/main.nf.test.snap
@@ -1,5 +1,40 @@
 {
-    "Should run without failures": {
+    "bacteroides_fragilis - genome - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,2204fb00277c287f5f3d82e28964aa03"
+                ],
+                "report": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,2204fb00277c287f5f3d82e28964aa03"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-19T21:06:27.483697023"
+    },
+    "bacteroides_fragilis - genome": {
         "content": [
             {
                 "0": [
@@ -28,6 +63,10 @@
                 ]
             }
         ],
-        "timestamp": "2023-10-15T10:06:00.77835847"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-19T21:06:20.036490495"
     }
 }
diff --git a/modules/nf-core/abricate/summary/tests/main.nf.test b/modules/nf-core/abricate/summary/tests/main.nf.test
@@ -7,6 +7,7 @@ nextflow_process {
     tag "modules_nfcore"
     tag "abricate"
     tag "abricate/summary"
+    tag "abricate/run"
 
     test("Should run without failures") {
 
@@ -21,6 +22,7 @@ nextflow_process {
                                 tuple([ id:'test2', single_end:false ],
                                     file(params.test_data['haemophilus_influenzae']['genome']['genome_fna_gz'], checkIfExists: true))
                             ])
+                input[1] = []
                 """
             }
             }