From 029d27178b46d5dd7b884b721d7ae5461fe3cc53 Mon Sep 17 00:00:00 2001 From: jasmezz Date: Thu, 16 Jan 2025 14:50:53 +0100 Subject: [PATCH] Remove wrong files --- .../rgi/wildcardannotation/environment.yml | 7 -- .../nf-core/rgi/wildcardannotation/main.nf | 60 ----------------- .../nf-core/rgi/wildcardannotation/meta.yml | 45 ------------- .../rgi/wildcardannotation/tests/main.nf.test | 66 ------------------- .../rgi/wildcardannotation/tests/tags.yml | 2 - 5 files changed, 180 deletions(-) delete mode 100644 modules/nf-core/rgi/wildcardannotation/environment.yml delete mode 100644 modules/nf-core/rgi/wildcardannotation/main.nf delete mode 100644 modules/nf-core/rgi/wildcardannotation/meta.yml delete mode 100644 modules/nf-core/rgi/wildcardannotation/tests/main.nf.test delete mode 100644 modules/nf-core/rgi/wildcardannotation/tests/tags.yml diff --git a/modules/nf-core/rgi/wildcardannotation/environment.yml b/modules/nf-core/rgi/wildcardannotation/environment.yml deleted file mode 100644 index b6c3b83135e..00000000000 --- a/modules/nf-core/rgi/wildcardannotation/environment.yml +++ /dev/null @@ -1,7 +0,0 @@ -name: rgi_wildcardannotation -channels: - - conda-forge - - bioconda - - defaults -dependencies: - - bioconda::rgi=6.0.3 diff --git a/modules/nf-core/rgi/wildcardannotation/main.nf b/modules/nf-core/rgi/wildcardannotation/main.nf deleted file mode 100644 index 9f1af5f478c..00000000000 --- a/modules/nf-core/rgi/wildcardannotation/main.nf +++ /dev/null @@ -1,60 +0,0 @@ -process RGI_WILDCARDANNOTATION { - 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(wildcard) - path(card_json) - - output: - path("wildcard_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 wildcard_annotation \\ - -i $wildcard \\ - --card_json $card_json \\ - -v - $args - - mkdir wildcard_database_processed - cp *.gz wildcard_database_processed - cp Variants-Download-README.txt wildcard_database_processed - - RGI_VERSION=\$(rgi main --version) - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - rgi: \$(echo \$RGI_VERSION) - END_VERSIONS - """ - - stub: - """ - touch card.fasta - touch card_all.fasta - - mkdir wildcard_database_processed - cp *.gz wildcard_database_processed - cp Variants-Download-README.txt wildcard_database_processed - - RGI_VERSION=\$(rgi main --version) - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - rgi: \$(echo \$RGI_VERSION) - END_VERSIONS - """ -} diff --git a/modules/nf-core/rgi/wildcardannotation/meta.yml b/modules/nf-core/rgi/wildcardannotation/meta.yml deleted file mode 100644 index 97820a7b7f1..00000000000 --- a/modules/nf-core/rgi/wildcardannotation/meta.yml +++ /dev/null @@ -1,45 +0,0 @@ -name: rgi_wildcardannotation -description: Preprocess the WildCARD 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 WildCARD database 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: - - wildcard: - type: directory - description: Directory containing the WildCARD database - pattern: "*/" - - card_json: - type: file - description: The obligatory card.json file of the CARD database (see RGI database documentation) -output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - db: - type: directory - description: Directory containing the processed WildCARD 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" diff --git a/modules/nf-core/rgi/wildcardannotation/tests/main.nf.test b/modules/nf-core/rgi/wildcardannotation/tests/main.nf.test deleted file mode 100644 index 8dd14d5db3f..00000000000 --- a/modules/nf-core/rgi/wildcardannotation/tests/main.nf.test +++ /dev/null @@ -1,66 +0,0 @@ -nextflow_process { - - name "Test Process RGI_WILDCARDANNOTATION" - script "../main.nf" - process "RGI_WILDCARDANNOTATION" - - tag "modules" - tag "modules_nfcore" - tag "rgi" - tag "rgi/wildcardannotation" - tag "untar" - - setup { - run("UNTAR") { - script "modules/nf-core/untar/main.nf" - process { - """ - file('https://card.mcmaster.ca/latest/variants', checkIfExists: true).copyTo('variants.tar.gz') - - input[0] = [ - [ ], - file("data.tar.gz") - ] - """ - } - } - } - - test("rgi/wildcardannotation") { - - when { - process { - """ - input[0] = UNTAR.out.untar.map{ it[1] } - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } - - test("rgi/wildcardannotation - stub") { - - options "-stub" - - when { - process { - """ - input[0] = UNTAR.out.untar.map{ it[1] } - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } -} diff --git a/modules/nf-core/rgi/wildcardannotation/tests/tags.yml b/modules/nf-core/rgi/wildcardannotation/tests/tags.yml deleted file mode 100644 index a4b9eb12472..00000000000 --- a/modules/nf-core/rgi/wildcardannotation/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -rgi/wildcardannotation: - - "modules/nf-core/rgi/wildcardannotation/**"