Update module: bakta/bakta (nf-core#4847)

* Add nf-test + remove pytest files

* Apply changes from code review

* Fix main.test.nf

* Update process label to increase memory/fix diamond error

* Stub tests only

* Increase memory (for CI checks to succeed)

* Fix config, activate test

* Increase memory

* Increase memory

* Activate singularity profile

* Exclude conda tests due to DIAMOND memory issue on conda

* Skip conda

* Skip conda CI check of dependency baktadbdownload

---------

Co-authored-by: James A. Fellows Yates <[email protected]>

.github/workflows/test.yml

@@ -476,6 +476,10 @@ jobs:
             tags: happy/sompy
           - profile: conda
             tags: backsub
+          - profile: conda
+            tags: bakta/bakta
+          - profile: conda
+            tags: bakta/baktadbdownload
           - profile: conda
             tags: bases2fastq
           - profile: conda

modules/nf-core/bakta/bakta/environment.yml

@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::bakta=1.8.2
+  - bioconda::bakta=1.9.2

modules/nf-core/bakta/bakta/main.nf

@@ -4,8 +4,8 @@ process BAKTA_BAKTA {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bakta:1.8.2--pyhdfd78af_0' :
-        'biocontainers/bakta:1.8.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/bakta:1.9.2--pyhdfd78af_0' :
+        'biocontainers/bakta:1.9.2--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(fasta)

modules/nf-core/bakta/bakta/tests/main.nf.test

@@ -0,0 +1,83 @@
+nextflow_process {
+
+    name "Test Process BAKTA_BAKTA"
+    script "../main.nf"
+    config "./nextflow.config"
+    process "BAKTA_BAKTA"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "bakta"
+    tag "bakta/bakta"
+    tag "bakta/baktadbdownload"
+
+    test("Bakta - bacteroides_fragilis - genome.fasta") {
+
+        setup {
+            run("BAKTA_BAKTADBDOWNLOAD") {
+                script "../../baktadbdownload/main.nf"
+                process {
+                    """
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """             
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true)
+                ]
+                input[1] = BAKTA_BAKTADBDOWNLOAD.out.db
+                input[2] = []
+                input[3] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.embl.get(0).get(1)).text.contains("/translation=\"MKNTLKIAILLIAIISMGHWMPVKQVCDLNSLSLQNVEALANGET") },
+                { assert path(process.out.faa.get(0).get(1)).text.contains("MKNTLKIAILLIAIISMGHWMPVKQVCDLNSLSLQNVEALANGETPNYTFCIGAGSVDCPIQHDKVKYVSQGFSLDY") },
+                { assert path(process.out.ffn.get(0).get(1)).text.contains("ATGAAAAACACTTTAAAAATAGCTATTCTTCTTATTGCTATTATTTCTATGGGGCATTGGATGCCTGTAAAACAAGT") },
+                { assert path(process.out.fna.get(0).get(1)).text.contains("TCTTTTTACTCATAATCTACTTTTATGATGTTAATTATTTTTTCCGTGTCTCTCTTTCGG") },
+                { assert path(process.out.gbff.get(0).get(1)).text.contains("/translation=\"MKNTLKIAILLIAIISMGHWMPVKQVCDLNSLSLQNVEALANGET") },
+                { assert path(process.out.gff.get(0).get(1)).text.contains("##sequence-region contig_1 1 2926") },
+                { assert path(process.out.hypotheticals_tsv.get(0).get(1)).text.contains("#Annotated with Bakta") },
+                { assert path(process.out.hypotheticals_faa.get(0).get(1)).text.contains("MKNLILVLGCFFFLISCQQTEKEKLEELVKNWNGKEVLL") },
+                { assert path(process.out.tsv.get(0).get(1)).text.contains("SO:0001217, UniRef:UniRef50_A0A0I9S7A3") },
+                { assert path(process.out.txt.get(0).get(1)).text.contains("Length: 1739120") },
+                { assert snapshot(process.out.versions).match("versions") }
+            )
+        }
+
+    }
+
+    test("Bakta - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """  
+                input[0] = [[id: 'stub'],file('stub')]
+                input[1] = []
+                input[2] = []
+                input[3] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}

modules/nf-core/bakta/bakta/tests/nextflow.config

@@ -0,0 +1,11 @@
+process {
+
+    withName: 'BAKTA_BAKTADBDOWNLOAD' {
+        ext.args = "--type light"
+    }
+
+    withName: 'BAKTA_BAKTA' {
+        memory = 15.4.GB
+    }
+
+}

modules/nf-core/bakta/bakta/tests/tags.yml

@@ -0,0 +1,2 @@
+bakta/bakta:
+  - "modules/nf-core/bakta/bakta/**"

modules/nf-core/bakta/baktadbdownload/tests/nextflow.config

@@ -1,7 +1,7 @@
 process {
 
-
     withName: 'BAKTA_BAKTADBDOWNLOAD' {
         ext.args = "--type light"
     }
+
 }

tests/config/pytest_modules.yml

@@ -85,9 +85,6 @@ atlasgeneannotationmanipulation/gtf2featureannotation:
 authentict/deam2cont:
   - modules/nf-core/authentict/deam2cont/**
   - tests/modules/nf-core/authentict/deam2cont/**
-bakta/bakta:
-  - modules/nf-core/bakta/bakta/**
-  - tests/modules/nf-core/bakta/bakta/**
 bam2fastx/bam2fastq:
   - modules/nf-core/bam2fastx/bam2fastq/**
   - tests/modules/nf-core/bam2fastx/bam2fastq/**