Update rgi/main to 6.0.3 (#4933)

* First attempt to include download of databases

* Update module files + add nf-test (almost working)

* Added stub + snapshot file + many fixes

* Make rgi/main work with CARD download

* Fix linting

* Update depency `hamronization/rgi`

* Fix command in `main.nf`

* Fix `hamronization/rgi` accordingly

* Removed DB download functionality

* Removed hamronization/rgi non-stub test

* Update meta.yml

* Add module rgi/cardannotation (not working yet)

* Make rgi/main tests work incl. dependency rgi/cardannotation

* Fix hamronization/rgi tests

* Update rgi/cardannotation snapfile

* Apply suggestions from code review

modules/nf-core/hamronization/rgi/tests/main.nf.test

@@ -9,22 +9,50 @@ nextflow_process {
     tag "hamronization"
     tag "hamronization/rgi"
     tag "rgi/main"
+    tag "rgi/cardannotation"
+    tag "untar"
 
     setup {
+
+        run("UNTAR") {
+            script "modules/nf-core/untar/main.nf"
+            process {
+            """
+            file('https://card.mcmaster.ca/latest/data', checkIfExists: true).copyTo('data.tar.gz')
+
+            input[0] = [
+                [ ],
+                file("data.tar.gz")
+            ]
+            """
+            }
+        }
+
+        run("RGI_CARDANNOTATION") {
+            script "modules/nf-core/rgi/cardannotation/main.nf"
+            process {
+                """
+                input[0] = UNTAR.out.untar.map{ it[1] }
+                """
+            }
+        }
+
         run("RGI_MAIN") {
-            script "../../../rgi/main/main.nf"
+            script "modules/nf-core/rgi/main/main.nf"
             process {
                 """
                 input[0] = [                                                                                                                                                                     
                     [ id:'test', single_end:false ], // meta map                                                                                                                              
                     file(params.test_data['haemophilus_influenzae']['genome']['genome_fna_gz'], checkIfExists: true)                                                                          
                 ]
+                input[1] = RGI_CARDANNOTATION.out.db
+                input[2] = []
                 """
             }
         }
     }
 
-    test("hamronization/amrfinderplus - haemophilus_influenzae - genome - fna.gz") {
+    test("hamronization/rgi - haemophilus_influenzae - genome - fna.gz") {
 
         when {
             process {
@@ -45,7 +73,7 @@ nextflow_process {
         }
     }
 
-    test("hamronization/amrfinderplus - haemophilus_influenzae - genome - fna.gz - stub") {
+    test("hamronization/rgi - haemophilus_influenzae - genome - fna.gz - stub") {
 
         options "-stub"
 

modules/nf-core/rgi/cardannotation/environment.yml

@@ -0,0 +1,7 @@
+name: rgi_cardannotation
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::rgi=6.0.3

modules/nf-core/rgi/cardannotation/main.nf

@@ -0,0 +1,61 @@
+process RGI_CARDANNOTATION {
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/rgi:6.0.3--pyha8f3691_0':
+        'biocontainers/rgi:6.0.3--pyha8f3691_0' }"
+
+    input:
+    path(card)
+
+    output:
+    path("card_database_processed") , emit: db
+    env RGI_VERSION                 , emit: tool_version
+    env DB_VERSION                  , emit: db_version
+    path "versions.yml"             , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+
+    """
+    rgi card_annotation \\
+        -i ${card}/card.json \\
+        $args
+
+    DB_VERSION=\$(ls card_database_*_all.fasta | sed "s/card_database_v\\([0-9].*[0-9]\\).*/\\1/")
+
+    mkdir card_database_processed
+    mv card*.fasta card_database_processed
+    cp ${card}/* card_database_processed
+
+    RGI_VERSION=\$(rgi main --version)
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        rgi: \$(echo \$RGI_VERSION)
+        rgi-database: \$(echo \$DB_VERSION)
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    touch card.fasta
+    touch card_all.fasta
+
+    mkdir card_database_processed
+    mv card*.fasta card_database_processed
+
+    RGI_VERSION=\$(rgi main --version)
+    DB_VERSION=stub_version
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        rgi: \$(echo \$RGI_VERSION)
+        rgi-database: \$(echo \$DB_VERSION)
+    END_VERSIONS
+    """
+}

modules/nf-core/rgi/cardannotation/meta.yml

@@ -0,0 +1,42 @@
+name: rgi_cardannotation
+description: Preprocess the CARD database for RGI to predict antibiotic resistance from protein or nucleotide data
+keywords:
+  - bacteria
+  - fasta
+  - antibiotic resistance
+tools:
+  - rgi:
+      description: This module preprocesses the downloaded Comprehensive Antibiotic Resistance Database (CARD) which can then be used as input for RGI.
+      homepage: https://card.mcmaster.ca
+      documentation: https://github.com/arpcard/rgi
+      tool_dev_url: https://github.com/arpcard/rgi
+      doi: "10.1093/nar/gkz935"
+      licence: ["https://card.mcmaster.ca/about"]
+input:
+  - card:
+      type: directory
+      description: Directory containing the CARD database
+      pattern: "*/"
+output:
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - db:
+      type: directory
+      description: Directory containing the processed CARD database files
+      pattern: "*/"
+  - tool_version:
+      type: string
+      description: The version of the tool in string format (useful for downstream tools such as hAMRronization)
+  - db_version:
+      type: string
+      description: The version of the used database in string format (useful for downstream tools such as hAMRronization)
+authors:
+  - "@rpetit3"
+  - "@jfy133"
+  - "@jasmezz"
+maintainers:
+  - "@rpetit3"
+  - "@jfy133"
+  - "@jasmezz"

modules/nf-core/rgi/cardannotation/tests/main.nf.test

@@ -0,0 +1,66 @@
+nextflow_process {
+
+    name "Test Process RGI_CARDANNOTATION"
+    script "../main.nf"
+    process "RGI_CARDANNOTATION"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "rgi"
+    tag "rgi/cardannotation"
+    tag "untar"
+
+    setup {
+        run("UNTAR") {
+            script "modules/nf-core/untar/main.nf"
+            process {
+            """
+            file('https://card.mcmaster.ca/latest/data', checkIfExists: true).copyTo('data.tar.gz')
+
+            input[0] = [
+                [ ],
+                file("data.tar.gz")
+            ]
+            """
+            }
+        }
+    }
+
+    test("rgi/cardannotation") {
+
+        when {
+            process {
+                """
+                input[0] = UNTAR.out.untar.map{ it[1] }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("rgi/cardannotation - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = UNTAR.out.untar.map{ it[1] }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}