diff --git a/CHANGELOG.md b/CHANGELOG.md index ebe08427..f25f21ed 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -22,6 +22,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | Tool | Previous Version | New Version | | --------- | ---------------- | ----------- | | antiSMASH | 7.1.0 | 8.0.1 | +| RGI | 6.0.3 | 6.0.5 | ### `Deprecated` diff --git a/README.md b/README.md index 18581214..b22e925b 100644 --- a/README.md +++ b/README.md @@ -18,6 +18,8 @@ [![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23funcscan-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/funcscan)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core) +![HiRSE Code Promo Badge](https://img.shields.io/badge/Promo-8db427?style=plastic&label=HiRSE&labelColor=005aa0&link=https%3A%2F%2Fgo.fzj.de%2FCodePromo) + ## Introduction **nf-core/funcscan** is a bioinformatics best-practice analysis pipeline for the screening of nucleotide sequences such as assembled contigs for functional genes. It currently features mining for antimicrobial peptides, antibiotic resistance genes and biosynthetic gene clusters. diff --git a/conf/test_bakta.config b/conf/test_bakta.config index 4cd2dacb..020eba81 100644 --- a/conf/test_bakta.config +++ b/conf/test_bakta.config @@ -14,7 +14,7 @@ process { resourceLimits = [ cpus: 4, memory: '15.GB', - time: '1.h' + time: '1.h', ] } @@ -33,5 +33,6 @@ params { amp_hmmsearch_models = params.pipelines_testdata_base_path + 'funcscan/hmms/mybacteriocin.hmm' run_arg_screening = true + arg_skip_deeparg = true arg_fargene_hmmmodel = 'class_a,class_b_1_2' } diff --git a/modules.json b/modules.json index 106fbd4d..5302c555 100644 --- a/modules.json +++ b/modules.json @@ -192,12 +192,12 @@ }, "rgi/cardannotation": { "branch": "master", - "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", + "git_sha": "531d8a465158c5842f416623017997462a240e16", "installed_by": ["modules"] }, "rgi/main": { "branch": "master", - "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", + "git_sha": "531d8a465158c5842f416623017997462a240e16", "installed_by": ["modules"] }, "seqkit/seq": { diff --git a/modules/nf-core/rgi/cardannotation/environment.yml b/modules/nf-core/rgi/cardannotation/environment.yml index a3169324..b6b2d343 100644 --- a/modules/nf-core/rgi/cardannotation/environment.yml +++ b/modules/nf-core/rgi/cardannotation/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::rgi=6.0.3 + - bioconda::rgi=6.0.5 diff --git a/modules/nf-core/rgi/cardannotation/main.nf b/modules/nf-core/rgi/cardannotation/main.nf index d2a814e0..0386ce20 100644 --- a/modules/nf-core/rgi/cardannotation/main.nf +++ b/modules/nf-core/rgi/cardannotation/main.nf @@ -2,18 +2,18 @@ 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_1': - 'biocontainers/rgi:6.0.3--pyha8f3691_1' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://depot.galaxyproject.org/singularity/rgi:6.0.5--pyh05cac1d_0' + : 'biocontainers/rgi:6.0.5--pyh05cac1d_0'}" input: - path(card) + 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 + 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 @@ -24,7 +24,7 @@ process RGI_CARDANNOTATION { """ rgi card_annotation \\ -i ${card}/card.json \\ - $args + ${args} DB_VERSION=\$(ls card_database_*_all.fasta | sed "s/card_database_v\\([0-9].*[0-9]\\).*/\\1/") diff --git a/modules/nf-core/rgi/cardannotation/meta.yml b/modules/nf-core/rgi/cardannotation/meta.yml index 8aff020f..6810661c 100644 --- a/modules/nf-core/rgi/cardannotation/meta.yml +++ b/modules/nf-core/rgi/cardannotation/meta.yml @@ -16,31 +16,33 @@ tools: licence: ["https://card.mcmaster.ca/about"] identifier: "" input: - - - card: + - card: + type: directory + description: Directory containing the CARD database + pattern: "*/" +output: + db: + - card_database_processed: type: directory - description: Directory containing the CARD database + description: Directory containing the processed CARD database files pattern: "*/" -output: - - db: - - card_database_processed: - type: directory - description: Directory containing the processed CARD database files - pattern: "*/" - - tool_version: - - RGI_VERSION: - type: string - description: The version of the tool in string format (useful for downstream - tools such as hAMRronization) - - db_version: - - DB_VERSION: - type: string - description: The version of the used database in string format (useful for downstream - tools such as hAMRronization) - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + tool_version: + - RGI_VERSION: + type: string + description: The version of the tool in string format (useful for downstream + tools such as hAMRronization) + db_version: + - DB_VERSION: + type: string + description: The version of the used database in string format (useful for downstream + tools such as hAMRronization) + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@rpetit3" - "@jfy133" diff --git a/modules/nf-core/rgi/cardannotation/tests/main.nf.test.snap b/modules/nf-core/rgi/cardannotation/tests/main.nf.test.snap index 74a2f428..2d1391b0 100644 --- a/modules/nf-core/rgi/cardannotation/tests/main.nf.test.snap +++ b/modules/nf-core/rgi/cardannotation/tests/main.nf.test.snap @@ -9,13 +9,13 @@ ] ], "1": [ - "6.0.3" + "6.0.5" ], "2": [ "stub_version" ], "3": [ - "versions.yml:md5,ff6d0eeef874d3a3cb6e823cd4610e2d" + "versions.yml:md5,c42c7e6566b41df0310a5a4c1fd8f949" ], "db": [ [ @@ -27,92 +27,94 @@ "stub_version" ], "tool_version": [ - "6.0.3" + "6.0.5" ], "versions": [ - "versions.yml:md5,ff6d0eeef874d3a3cb6e823cd4610e2d" + "versions.yml:md5,c42c7e6566b41df0310a5a4c1fd8f949" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2024-02-19T23:33:34.376943812" + "timestamp": "2025-09-03T10:10:40.229702375" }, "rgi/cardannotation": { "content": [ { "0": [ [ - "CARD-Download-README.txt:md5,ca330e1d89e3a97ac6f50c86a8ca5c34", - "aro_categories.tsv:md5,cdefc6d0169bc7a077020022be68e38b", - "aro_categories_index.tsv:md5,f99f2fed0cf357c7c3e7e39e4b880ca2", - "aro_index.tsv:md5,3052f507daff81356f4e985025928217", - "card.json:md5,c9550768ded14c01a56c98e3c4931176", - "card_database_v3.3.0.fasta:md5,b3fd50f7946aed8009c131a3c1454728", - "card_database_v3.3.0_all.fasta:md5,81ffb872759695abd1023c0b5f8fe0d5", - "nucleotide_fasta_protein_homolog_model.fasta:md5,93fcfd413dda3056612f725d5bc06356", - "nucleotide_fasta_protein_knockout_model.fasta:md5,ff476b358ef70da53acf4602568a9b9b", - "nucleotide_fasta_protein_overexpression_model.fasta:md5,68937e587c880153400fa8203f6a90d5", - "nucleotide_fasta_protein_variant_model.fasta:md5,58a4644e05df59af7a918f25b61e5a22", + "CARD-Download-README.txt:md5,b57364cc1a5fab0541e13a01fabe5dea", + "PMID.tsv:md5,e3ce79c4b5dcf0a9e3117ed683f96e54", + "aro_categories.tsv:md5,6f9c4b0410b9e2b3cf5867a2a3f1db07", + "aro_categories_index.tsv:md5,d5fbc673c0de6601b07c8016b3909f8e", + "aro_index.tsv:md5,0f183c7869876fa32c8f86aade0df7b5", + "card.json:md5,72156d00155f69e637664bfb5d3b5395", + "card_database_v4.0.1.fasta:md5,5ead0b239c312ebb068a3b5aa9676b2d", + "card_database_v4.0.1_all.fasta:md5,f389ce15fac30e9ab394ca8a49f6451f", + "nucleotide_fasta_protein_homolog_model.fasta:md5,696d1aa4f04bd08fc4bdeea33ab9db43", + "nucleotide_fasta_protein_knockout_model.fasta:md5,d8224ce019ad69a041d83ccf7877b4e0", + "nucleotide_fasta_protein_overexpression_model.fasta:md5,80a1e7957c79d311446e06c6dd49db8e", + "nucleotide_fasta_protein_variant_model.fasta:md5,7450e559045c9d1d8f13c73054c64f4c", "nucleotide_fasta_rRNA_gene_variant_model.fasta:md5,bd53f46d630f652c9f6b7584c2126e1f", - "protein_fasta_protein_homolog_model.fasta:md5,63a89932339a665c390cebd50627f19b", - "protein_fasta_protein_knockout_model.fasta:md5,6b259399e3eae3f23eaa421bbba6ba25", - "protein_fasta_protein_overexpression_model.fasta:md5,758b753b821789147cdd795c654940ad", - "protein_fasta_protein_variant_model.fasta:md5,7fb7bbf0001837a59504d406ece90807", - "shortname_antibiotics.tsv:md5,86eaefabf930b91bf08d3630abdd0a3b", - "shortname_pathogens.tsv:md5,4a69150eeec95693727f0cc178c0770a", - "snps.txt:md5,2f7a6bea480a7e3a6fc7f7f763c4b3fe" + "protein_fasta_protein_homolog_model.fasta:md5,36ea300133fd7c5a45de2fee4c5050bf", + "protein_fasta_protein_knockout_model.fasta:md5,f16667df70d1a5f910d3ae45f5250c3d", + "protein_fasta_protein_overexpression_model.fasta:md5,723e8762be5c96aed8c379a6499cecee", + "protein_fasta_protein_variant_model.fasta:md5,8c02d8fc84c9a90953f8534355244019", + "shortname_antibiotics.tsv:md5,9a4ba742fd8a3a49c7f50744001a4129", + "shortname_pathogens.tsv:md5,5211712be4f4c3306cbe4052cafae1d7", + "snps.txt:md5,529d4fdb74c8940c0930ec1a7a6d4980" ] ], "1": [ - "6.0.3" + "6.0.5" ], "2": [ - "3.3.0" + "4.0.1" ], "3": [ - "versions.yml:md5,51bd8e4be5e532c5bdcfbb67c06dd808" + "versions.yml:md5,bbd7b05923d280ece1cc3c426aa98ea9" ], "db": [ [ - "CARD-Download-README.txt:md5,ca330e1d89e3a97ac6f50c86a8ca5c34", - "aro_categories.tsv:md5,cdefc6d0169bc7a077020022be68e38b", - "aro_categories_index.tsv:md5,f99f2fed0cf357c7c3e7e39e4b880ca2", - "aro_index.tsv:md5,3052f507daff81356f4e985025928217", - "card.json:md5,c9550768ded14c01a56c98e3c4931176", - "card_database_v3.3.0.fasta:md5,b3fd50f7946aed8009c131a3c1454728", - "card_database_v3.3.0_all.fasta:md5,81ffb872759695abd1023c0b5f8fe0d5", - "nucleotide_fasta_protein_homolog_model.fasta:md5,93fcfd413dda3056612f725d5bc06356", - "nucleotide_fasta_protein_knockout_model.fasta:md5,ff476b358ef70da53acf4602568a9b9b", - "nucleotide_fasta_protein_overexpression_model.fasta:md5,68937e587c880153400fa8203f6a90d5", - "nucleotide_fasta_protein_variant_model.fasta:md5,58a4644e05df59af7a918f25b61e5a22", + "CARD-Download-README.txt:md5,b57364cc1a5fab0541e13a01fabe5dea", + "PMID.tsv:md5,e3ce79c4b5dcf0a9e3117ed683f96e54", + "aro_categories.tsv:md5,6f9c4b0410b9e2b3cf5867a2a3f1db07", + "aro_categories_index.tsv:md5,d5fbc673c0de6601b07c8016b3909f8e", + "aro_index.tsv:md5,0f183c7869876fa32c8f86aade0df7b5", + "card.json:md5,72156d00155f69e637664bfb5d3b5395", + "card_database_v4.0.1.fasta:md5,5ead0b239c312ebb068a3b5aa9676b2d", + "card_database_v4.0.1_all.fasta:md5,f389ce15fac30e9ab394ca8a49f6451f", + "nucleotide_fasta_protein_homolog_model.fasta:md5,696d1aa4f04bd08fc4bdeea33ab9db43", + "nucleotide_fasta_protein_knockout_model.fasta:md5,d8224ce019ad69a041d83ccf7877b4e0", + "nucleotide_fasta_protein_overexpression_model.fasta:md5,80a1e7957c79d311446e06c6dd49db8e", + "nucleotide_fasta_protein_variant_model.fasta:md5,7450e559045c9d1d8f13c73054c64f4c", "nucleotide_fasta_rRNA_gene_variant_model.fasta:md5,bd53f46d630f652c9f6b7584c2126e1f", - "protein_fasta_protein_homolog_model.fasta:md5,63a89932339a665c390cebd50627f19b", - "protein_fasta_protein_knockout_model.fasta:md5,6b259399e3eae3f23eaa421bbba6ba25", - "protein_fasta_protein_overexpression_model.fasta:md5,758b753b821789147cdd795c654940ad", - "protein_fasta_protein_variant_model.fasta:md5,7fb7bbf0001837a59504d406ece90807", - "shortname_antibiotics.tsv:md5,86eaefabf930b91bf08d3630abdd0a3b", - "shortname_pathogens.tsv:md5,4a69150eeec95693727f0cc178c0770a", - "snps.txt:md5,2f7a6bea480a7e3a6fc7f7f763c4b3fe" + "protein_fasta_protein_homolog_model.fasta:md5,36ea300133fd7c5a45de2fee4c5050bf", + "protein_fasta_protein_knockout_model.fasta:md5,f16667df70d1a5f910d3ae45f5250c3d", + "protein_fasta_protein_overexpression_model.fasta:md5,723e8762be5c96aed8c379a6499cecee", + "protein_fasta_protein_variant_model.fasta:md5,8c02d8fc84c9a90953f8534355244019", + "shortname_antibiotics.tsv:md5,9a4ba742fd8a3a49c7f50744001a4129", + "shortname_pathogens.tsv:md5,5211712be4f4c3306cbe4052cafae1d7", + "snps.txt:md5,529d4fdb74c8940c0930ec1a7a6d4980" ] ], "db_version": [ - "3.3.0" + "4.0.1" ], "tool_version": [ - "6.0.3" + "6.0.5" ], "versions": [ - "versions.yml:md5,51bd8e4be5e532c5bdcfbb67c06dd808" + "versions.yml:md5,bbd7b05923d280ece1cc3c426aa98ea9" ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nextflow": "25.04.6" }, - "timestamp": "2024-12-17T19:00:14.248138522" + "timestamp": "2025-09-03T10:10:17.719519729" } } \ No newline at end of file diff --git a/modules/nf-core/rgi/cardannotation/tests/tags.yml b/modules/nf-core/rgi/cardannotation/tests/tags.yml deleted file mode 100644 index 02c2de0b..00000000 --- a/modules/nf-core/rgi/cardannotation/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -rgi/cardannotation: - - "modules/nf-core/rgi/cardannotation/**" diff --git a/modules/nf-core/rgi/main/environment.yml b/modules/nf-core/rgi/main/environment.yml index a3169324..b6b2d343 100644 --- a/modules/nf-core/rgi/main/environment.yml +++ b/modules/nf-core/rgi/main/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::rgi=6.0.3 + - bioconda::rgi=6.0.5 diff --git a/modules/nf-core/rgi/main/main.nf b/modules/nf-core/rgi/main/main.nf index 287875fa..a796460c 100644 --- a/modules/nf-core/rgi/main/main.nf +++ b/modules/nf-core/rgi/main/main.nf @@ -1,31 +1,33 @@ process RGI_MAIN { - tag "$meta.id" + tag "${meta.id}" label 'process_medium' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/rgi:6.0.3--pyha8f3691_1': - 'biocontainers/rgi:6.0.3--pyha8f3691_1' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://depot.galaxyproject.org/singularity/rgi:6.0.5--pyh05cac1d_0' + : 'biocontainers/rgi:6.0.5--pyh05cac1d_0'}" input: tuple val(meta), path(fasta) - path(card) - path(wildcard) + path card + path wildcard output: tuple val(meta), path("*.json"), emit: json - tuple val(meta), path("*.txt") , emit: tsv - tuple val(meta), path("temp/") , emit: tmp - env RGI_VERSION , emit: tool_version - env DB_VERSION , emit: db_version - path "versions.yml" , emit: versions + tuple val(meta), path("*.txt"), emit: tsv + tuple val(meta), path("temp/"), emit: tmp + 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 ?: '' // This customizes the command: rgi load - def args2 = task.ext.args2 ?: '' // This customizes the command: rgi main + def args = task.ext.args ?: '' + // This customizes the command: rgi load + def args2 = task.ext.args2 ?: '' + // This customizes the command: rgi main def prefix = task.ext.prefix ?: "${meta.id}" def load_wildcard = "" @@ -45,19 +47,19 @@ process RGI_MAIN { rgi \\ load \\ - $args \\ + ${args} \\ --card_json ${card}/card.json \\ --debug --local \\ --card_annotation ${card}/card_database_v\$DB_VERSION.fasta \\ --card_annotation_all_models ${card}/card_database_v\$DB_VERSION\\_all.fasta \\ - $load_wildcard + ${load_wildcard} rgi \\ main \\ - $args2 \\ - --num_threads $task.cpus \\ - --output_file $prefix \\ - --input_sequence $fasta + ${args2} \\ + --num_threads ${task.cpus} \\ + --output_file ${prefix} \\ + --input_sequence ${fasta} mkdir temp/ for FILE in *.xml *.fsa *.{nhr,nin,nsq} *.draft *.potentialGenes *{variant,rrna,protein,predictedGenes,overexpression,homolog}.json; do [[ -e \$FILE ]] && mv \$FILE temp/; done diff --git a/modules/nf-core/rgi/main/meta.yml b/modules/nf-core/rgi/main/meta.yml index 9d9836c0..f8b102f6 100644 --- a/modules/nf-core/rgi/main/meta.yml +++ b/modules/nf-core/rgi/main/meta.yml @@ -28,21 +28,22 @@ input: type: file description: Nucleotide or protein sequences in FASTA format pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}" - - - card: - type: directory - description: Directory containing the CARD database. This is expected to be - the unarchived but otherwise unaltered download folder (see RGI documentation - for download instructions). - pattern: "*/" - - - wildcard: - type: directory - description: Directory containing the WildCARD database (optional). This is - expected to be the unarchived but otherwise unaltered download folder (see - RGI documentation for download instructions). - pattern: "*/" + ontologies: [] + - card: + type: directory + description: Directory containing the CARD database. This is expected to be the + unarchived but otherwise unaltered download folder (see RGI documentation for + download instructions). + pattern: "*/" + - wildcard: + type: directory + description: Directory containing the WildCARD database (optional). This is expected + to be the unarchived but otherwise unaltered download folder (see RGI documentation + for download instructions). + pattern: "*/" output: - - json: - - meta: + json: + - - meta: type: map description: | Groovy Map containing sample information @@ -51,8 +52,10 @@ output: type: file description: JSON formatted file with RGI results pattern: "*.{json}" - - tsv: - - meta: + ontologies: + - edam: http://edamontology.org/format_3464 # JSON + tsv: + - - meta: type: map description: | Groovy Map containing sample information @@ -61,8 +64,9 @@ output: type: file description: Tab-delimited file with RGI results pattern: "*.{txt}" - - tmp: - - meta: + ontologies: [] + tmp: + - - meta: type: map description: | Groovy Map containing sample information @@ -71,21 +75,23 @@ output: type: directory description: Directory containing various intermediate files pattern: "temp/" - - tool_version: - - RGI_VERSION: - type: string - description: The version of the tool in string format (useful for downstream - tools such as hAMRronization) - - db_version: - - DB_VERSION: - type: string - description: The version of the used database in string format (useful for downstream - tools such as hAMRronization) - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + tool_version: + - RGI_VERSION: + type: string + description: The version of the tool in string format (useful for downstream + tools such as hAMRronization) + db_version: + - DB_VERSION: + type: string + description: The version of the used database in string format (useful for downstream + tools such as hAMRronization) + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@rpetit3" - "@jfy133" diff --git a/modules/nf-core/rgi/main/tests/main.nf.test.snap b/modules/nf-core/rgi/main/tests/main.nf.test.snap index 35b4f7cf..52d455e7 100644 --- a/modules/nf-core/rgi/main/tests/main.nf.test.snap +++ b/modules/nf-core/rgi/main/tests/main.nf.test.snap @@ -32,13 +32,13 @@ ] ], "3": [ - "6.0.3" + "6.0.5" ], "4": [ "stub_version" ], "5": [ - "versions.yml:md5,f77ce9bdc8d309c9d6f7ec63bd53f5cf" + "versions.yml:md5,b0808f9aef5a00d6542969c6dbd1c891" ], "db_version": [ "stub_version" @@ -64,7 +64,7 @@ ] ], "tool_version": [ - "6.0.3" + "6.0.5" ], "tsv": [ [ @@ -76,20 +76,20 @@ ] ], "versions": [ - "versions.yml:md5,f77ce9bdc8d309c9d6f7ec63bd53f5cf" + "versions.yml:md5,b0808f9aef5a00d6542969c6dbd1c891" ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.2" + "nextflow": "25.04.6" }, - "timestamp": "2024-12-10T13:33:59.209306934" + "timestamp": "2025-09-03T10:03:18.046807023" }, "rgi/main - haemophilus_influenzae - genome_fna_gz": { "content": [ [ - "versions.yml:md5,306dec3569e66a74bff07184f2f801ec" + "versions.yml:md5,1c882aa66647fa7275d0c9fd6d2dda5f" ], [ [ @@ -97,7 +97,7 @@ "id": "test", "single_end": false }, - "test.txt:md5,5854d6bef754d91da80980e96b6a054b" + "test.txt:md5,9d7754551163e020beed52a8bc14ce83" ] ], [ @@ -106,7 +106,7 @@ "id": "test", "single_end": false }, - "test.json:md5,f9ca00ea1ff6e733c7c25bb2dfd65128" + "test.json:md5,6c403fb8e2f24b7c88be27ba5a30ca70" ] ], [ @@ -128,16 +128,16 @@ "genome.fna.gz.temp.uncompressed.fsa.temp.variant.json" ], [ - "6.0.3" + "6.0.5" ], [ - "3.3.0" + "4.0.1" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.2" + "nextflow": "25.04.6" }, - "timestamp": "2024-12-10T13:33:40.479165988" + "timestamp": "2025-09-03T10:03:00.004608398" } } \ No newline at end of file diff --git a/modules/nf-core/rgi/main/tests/tags.yml b/modules/nf-core/rgi/main/tests/tags.yml deleted file mode 100644 index e68ad8a2..00000000 --- a/modules/nf-core/rgi/main/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -rgi/main: - - "modules/nf-core/rgi/main/**" diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 461f61a2..2106fe7e 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -23,7 +23,7 @@ "@type": "Dataset", "creativeWorkStatus": "InProgress", "datePublished": "2025-07-08T10:27:35+00:00", - "description": "

\n \n \n \"nf-core/funcscan\"\n \n

\n\n[![GitHub Actions CI Status](https://github.com/nf-core/funcscan/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/funcscan/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/funcscan/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/funcscan/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/funcscan/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7643099-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7643099)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.10.5-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/funcscan)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23funcscan-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/funcscan)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/funcscan** is a bioinformatics best-practice analysis pipeline for the screening of nucleotide sequences such as assembled contigs for functional genes. It currently features mining for antimicrobial peptides, antibiotic resistance genes and biosynthetic gene clusters.\n\nThe pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!\n\nOn release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/funcscan/results).\n\nThe nf-core/funcscan AWS full test dataset are contigs generated by the MGnify service from the ENA. We used contigs generated from assemblies of chicken cecum shotgun metagenomes (study accession: MGYS00005631).\n\n## Pipeline summary\n\n1. Quality control of input sequences with [`SeqKit`](https://bioinf.shenwei.me/seqkit/)\n2. Taxonomic classification of contigs of **prokaryotic origin** with [`MMseqs2`](https://github.com/soedinglab/MMseqs2)\n3. Annotation of assembled prokaryotic contigs with [`Prodigal`](https://github.com/hyattpd/Prodigal), [`Pyrodigal`](https://github.com/althonos/pyrodigal), [`Prokka`](https://github.com/tseemann/prokka), or [`Bakta`](https://github.com/oschwengers/bakta)\n4. Annotation of coding sequences from 3. to obtain general protein families and domains with [`InterProScan`](https://github.com/ebi-pf-team/interproscan)\n5. Screening contigs for antimicrobial peptide-like sequences with [`ampir`](https://cran.r-project.org/web/packages/ampir/index.html), [`Macrel`](https://github.com/BigDataBiology/macrel), [`HMMER`](http://hmmer.org/), [`AMPlify`](https://github.com/bcgsc/AMPlify)\n6. Screening contigs for antibiotic resistant gene-like sequences with [`ABRicate`](https://github.com/tseemann/abricate), [`AMRFinderPlus`](https://github.com/ncbi/amr), [`fARGene`](https://github.com/fannyhb/fargene), [`RGI`](https://card.mcmaster.ca/analyze/rgi), [`DeepARG`](https://bench.cs.vt.edu/deeparg). [`argNorm`](https://github.com/BigDataBiology/argNorm) is used to map the outputs of `DeepARG`, `AMRFinderPlus`, and `ABRicate` to the [`Antibiotic Resistance Ontology`](https://www.ebi.ac.uk/ols4/ontologies/aro) for consistent ARG classification terms.\n7. Screening contigs for biosynthetic gene cluster-like sequences with [`antiSMASH`](https://antismash.secondarymetabolites.org), [`DeepBGC`](https://github.com/Merck/deepbgc), [`GECCO`](https://gecco.embl.de/), [`HMMER`](http://hmmer.org/)\n8. Creating aggregated reports for all samples across the workflows with [`AMPcombi`](https://github.com/Darcy220606/AMPcombi) for AMPs, [`hAMRonization`](https://github.com/pha4ge/hAMRonization) for ARGs, and [`comBGC`](https://raw.githubusercontent.com/nf-core/funcscan/master/bin/comBGC.py) for BGCs\n9. Software version and methods text reporting with [`MultiQC`](http://multiqc.info/)\n\n![funcscan metro workflow](docs/images/funcscan_metro_workflow.png)\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fasta\nCONTROL_REP1,AEG588A1_001.fasta\nCONTROL_REP2,AEG588A1_002.fasta\nCONTROL_REP3,AEG588A1_003.fasta\n```\n\nEach row represents a (multi-)fasta file of assembled contig sequences.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/funcscan \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \\\n --run_amp_screening \\\n --run_arg_screening \\\n --run_bgc_screening\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/funcscan/usage) and the [parameter documentation](https://nf-co.re/funcscan/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/funcscan/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/funcscan/output).\n\n## Credits\n\nnf-core/funcscan was originally written by Jasmin Frangenberg, Anan Ibrahim, Louisa Perelo, Moritz E. Beber, James A. Fellows Yates.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\nAdam Talbot, Alexandru Mizeranschi, Hugo Tavares, J\u00falia Mir Pedrol, Martin Klapper, Mehrdad Jaberi, Robert Syme, Rosa Herbst, Vedanth Ramji, @Microbion.\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#funcscan` channel](https://nfcore.slack.com/channels/funcscan) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/funcscan for your analysis, please cite it using the following doi: [10.5281/zenodo.7643099](https://doi.org/10.5281/zenodo.7643099)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", + "description": "

\n \n \n \"nf-core/funcscan\"\n \n

\n\n[![GitHub Actions CI Status](https://github.com/nf-core/funcscan/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/funcscan/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/funcscan/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/funcscan/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/funcscan/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7643099-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7643099)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.10.5-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/funcscan)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23funcscan-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/funcscan)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n![HiRSE Code Promo Badge](https://img.shields.io/badge/Promo-8db427?style=plastic&label=HiRSE&labelColor=005aa0&link=https%3A%2F%2Fgo.fzj.de%2FCodePromo)\n\n## Introduction\n\n**nf-core/funcscan** is a bioinformatics best-practice analysis pipeline for the screening of nucleotide sequences such as assembled contigs for functional genes. It currently features mining for antimicrobial peptides, antibiotic resistance genes and biosynthetic gene clusters.\n\nThe pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!\n\nOn release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/funcscan/results).\n\nThe nf-core/funcscan AWS full test dataset are contigs generated by the MGnify service from the ENA. We used contigs generated from assemblies of chicken cecum shotgun metagenomes (study accession: MGYS00005631).\n\n## Pipeline summary\n\n1. Quality control of input sequences with [`SeqKit`](https://bioinf.shenwei.me/seqkit/)\n2. Taxonomic classification of contigs of **prokaryotic origin** with [`MMseqs2`](https://github.com/soedinglab/MMseqs2)\n3. Annotation of assembled prokaryotic contigs with [`Prodigal`](https://github.com/hyattpd/Prodigal), [`Pyrodigal`](https://github.com/althonos/pyrodigal), [`Prokka`](https://github.com/tseemann/prokka), or [`Bakta`](https://github.com/oschwengers/bakta)\n4. Annotation of coding sequences from 3. to obtain general protein families and domains with [`InterProScan`](https://github.com/ebi-pf-team/interproscan)\n5. Screening contigs for antimicrobial peptide-like sequences with [`ampir`](https://cran.r-project.org/web/packages/ampir/index.html), [`Macrel`](https://github.com/BigDataBiology/macrel), [`HMMER`](http://hmmer.org/), [`AMPlify`](https://github.com/bcgsc/AMPlify)\n6. Screening contigs for antibiotic resistant gene-like sequences with [`ABRicate`](https://github.com/tseemann/abricate), [`AMRFinderPlus`](https://github.com/ncbi/amr), [`fARGene`](https://github.com/fannyhb/fargene), [`RGI`](https://card.mcmaster.ca/analyze/rgi), [`DeepARG`](https://bench.cs.vt.edu/deeparg). [`argNorm`](https://github.com/BigDataBiology/argNorm) is used to map the outputs of `DeepARG`, `AMRFinderPlus`, and `ABRicate` to the [`Antibiotic Resistance Ontology`](https://www.ebi.ac.uk/ols4/ontologies/aro) for consistent ARG classification terms.\n7. Screening contigs for biosynthetic gene cluster-like sequences with [`antiSMASH`](https://antismash.secondarymetabolites.org), [`DeepBGC`](https://github.com/Merck/deepbgc), [`GECCO`](https://gecco.embl.de/), [`HMMER`](http://hmmer.org/)\n8. Creating aggregated reports for all samples across the workflows with [`AMPcombi`](https://github.com/Darcy220606/AMPcombi) for AMPs, [`hAMRonization`](https://github.com/pha4ge/hAMRonization) for ARGs, and [`comBGC`](https://raw.githubusercontent.com/nf-core/funcscan/master/bin/comBGC.py) for BGCs\n9. Software version and methods text reporting with [`MultiQC`](http://multiqc.info/)\n\n![funcscan metro workflow](docs/images/funcscan_metro_workflow.png)\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fasta\nCONTROL_REP1,AEG588A1_001.fasta\nCONTROL_REP2,AEG588A1_002.fasta\nCONTROL_REP3,AEG588A1_003.fasta\n```\n\nEach row represents a (multi-)fasta file of assembled contig sequences.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/funcscan \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \\\n --run_amp_screening \\\n --run_arg_screening \\\n --run_bgc_screening\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/funcscan/usage) and the [parameter documentation](https://nf-co.re/funcscan/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/funcscan/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/funcscan/output).\n\n## Credits\n\nnf-core/funcscan was originally written by Jasmin Frangenberg, Anan Ibrahim, Louisa Perelo, Moritz E. Beber, James A. Fellows Yates.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\nAdam Talbot, Alexandru Mizeranschi, Hugo Tavares, J\u00falia Mir Pedrol, Martin Klapper, Mehrdad Jaberi, Robert Syme, Rosa Herbst, Vedanth Ramji, @Microbion.\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#funcscan` channel](https://nfcore.slack.com/channels/funcscan) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/funcscan for your analysis, please cite it using the following doi: [10.5281/zenodo.7643099](https://doi.org/10.5281/zenodo.7643099)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", "hasPart": [ { "@id": "main.nf" diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index a2f71420..8f4731c0 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -120,11 +120,11 @@ "pyrodigal": "3.6.3" }, "RGI_CARDANNOTATION": { - "rgi": "6.0.3", + "rgi": "6.0.5", "rgi-database": "4.0.1" }, "RGI_MAIN": { - "rgi": "6.0.3", + "rgi": "6.0.5", "rgi-database": "4.0.1" }, "UNTAR_CARD": { @@ -137,20 +137,20 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "25.04.3" + "nextflow": "25.04.6" }, - "timestamp": "2025-06-18T09:03:18.913706717" + "timestamp": "2025-09-03T12:55:25.887393129" }, "rgi": { "content": [ - "sample_1.txt:md5,fce130af51f93cccfc09ddaf9caf623f", - "sample_2.txt:md5,fce130af51f93cccfc09ddaf9caf623f" + "sample_1.txt:md5,601f0a16c0e999c2c5272d81f61bdf2f", + "sample_2.txt:md5,601f0a16c0e999c2c5272d81f61bdf2f" ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nextflow": "25.04.6" }, - "timestamp": "2025-06-12T13:50:59.970056092" + "timestamp": "2025-09-03T12:55:25.957102881" }, "deeparg_tsv_ARG": { "content": [ diff --git a/tests/test_bakta.nf.test b/tests/test_bakta.nf.test index 2536b3b5..d1ce37f7 100644 --- a/tests/test_bakta.nf.test +++ b/tests/test_bakta.nf.test @@ -61,18 +61,6 @@ nextflow_pipeline { path("$outputDir/reports/ampcombi2/Ampcombi_complete.log") ).match("ampcombi_logfiles") }, - // DeepARG - { assert snapshot( - path("$outputDir/arg/deeparg/sample_1/sample_1.align.daa.tsv"), - path("$outputDir/arg/deeparg/sample_2/sample_2.align.daa.tsv"), - path("$outputDir/arg/deeparg/sample_1/sample_1.mapping.ARG"), - path("$outputDir/arg/deeparg/sample_2/sample_2.mapping.ARG") - ).match("deeparg_tsv_ARG") }, - { assert file("$outputDir/arg/deeparg/sample_1/sample_1.align.daa").name }, - { assert file("$outputDir/arg/deeparg/sample_2/sample_2.align.daa").name }, - { assert path("$outputDir/arg/deeparg/sample_1/sample_1.mapping.potential.ARG").text.contains("#ARG") }, - { assert path("$outputDir/arg/deeparg/sample_2/sample_2.mapping.potential.ARG").text.contains("#ARG") }, - // ABRicate { assert snapshot( path("$outputDir/arg/abricate/sample_1/sample_1.txt"), diff --git a/tests/test_bakta.nf.test.snap b/tests/test_bakta.nf.test.snap index 21e6633b..188850b1 100644 --- a/tests/test_bakta.nf.test.snap +++ b/tests/test_bakta.nf.test.snap @@ -35,27 +35,14 @@ }, "rgi": { "content": [ - "sample_1.txt:md5,fce130af51f93cccfc09ddaf9caf623f", - "sample_2.txt:md5,fce130af51f93cccfc09ddaf9caf623f" + "sample_1.txt:md5,601f0a16c0e999c2c5272d81f61bdf2f", + "sample_2.txt:md5,601f0a16c0e999c2c5272d81f61bdf2f" ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-23T16:51:37.292595392" - }, - "deeparg_tsv_ARG": { - "content": [ - "sample_1.align.daa.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", - "sample_2.align.daa.tsv:md5,4557fadca3f90ccb037b59558dddd528", - "sample_1.mapping.ARG:md5,0e049e99eab4c55666062df21707d5b9", - "sample_2.mapping.ARG:md5,0e049e99eab4c55666062df21707d5b9" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2024-07-23T16:51:37.245901486" + "timestamp": "2025-09-03T13:09:42.479392004" }, "ampir": { "content": [ diff --git a/tests/test_preannotated.nf.test.snap b/tests/test_preannotated.nf.test.snap index 2dcf4da9..aa88fd91 100644 --- a/tests/test_preannotated.nf.test.snap +++ b/tests/test_preannotated.nf.test.snap @@ -13,15 +13,15 @@ }, "rgi": { "content": [ - "sample_1.txt:md5,ff8f179d06d8566d8cf779fc7d1f4955", - "sample_2.txt:md5,cc4ae1fb9e0d5f79ef5105d640c7b748", - "sample_3.txt:md5,ff8f179d06d8566d8cf779fc7d1f4955" + "sample_1.txt:md5,81ec2a38460c0f819bdf292b2b1578d3", + "sample_2.txt:md5,e6d448a8a75f4e86efa6eaabebeb16a8", + "sample_3.txt:md5,81ec2a38460c0f819bdf292b2b1578d3" ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nextflow": "25.04.6" }, - "timestamp": "2025-03-04T13:44:42.337377281" + "timestamp": "2025-09-03T11:52:36.96182499" }, "deeparg": { "content": [ diff --git a/tests/test_prokka.nf.test.snap b/tests/test_prokka.nf.test.snap index 4e30230d..bd14dd26 100644 --- a/tests/test_prokka.nf.test.snap +++ b/tests/test_prokka.nf.test.snap @@ -35,14 +35,14 @@ }, "rgi": { "content": [ - "sample_1.txt:md5,fce130af51f93cccfc09ddaf9caf623f", - "sample_2.txt:md5,fce130af51f93cccfc09ddaf9caf623f" + "sample_1.txt:md5,601f0a16c0e999c2c5272d81f61bdf2f", + "sample_2.txt:md5,601f0a16c0e999c2c5272d81f61bdf2f" ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2024-07-24T12:53:09.964420301" + "timestamp": "2025-09-04T10:45:23.391758711" }, "deeparg_tsv_ARG": { "content": [ diff --git a/tests/test_taxonomy_bakta.nf.test b/tests/test_taxonomy_bakta.nf.test index bca158c6..542248a1 100644 --- a/tests/test_taxonomy_bakta.nf.test +++ b/tests/test_taxonomy_bakta.nf.test @@ -7,7 +7,7 @@ nextflow_pipeline { tag "test_taxonomy_bakta" profile "test_taxonomy_bakta" - test("-profile test_taxonomy") { + test("-profile test_taxonomy_bakta") { when { params { diff --git a/tests/test_taxonomy_bakta.nf.test.snap b/tests/test_taxonomy_bakta.nf.test.snap index c406c942..93649936 100644 --- a/tests/test_taxonomy_bakta.nf.test.snap +++ b/tests/test_taxonomy_bakta.nf.test.snap @@ -24,14 +24,14 @@ }, "rgi": { "content": [ - "sample_1.txt:md5,fce130af51f93cccfc09ddaf9caf623f", - "sample_2.txt:md5,fce130af51f93cccfc09ddaf9caf623f" + "sample_1.txt:md5,601f0a16c0e999c2c5272d81f61bdf2f", + "sample_2.txt:md5,601f0a16c0e999c2c5272d81f61bdf2f" ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2024-07-24T13:19:30.025771" + "timestamp": "2025-09-04T13:26:19.457462948" }, "ampir": { "content": [ diff --git a/tests/test_taxonomy_prokka.nf.test.snap b/tests/test_taxonomy_prokka.nf.test.snap index c00c3286..e05977fb 100644 --- a/tests/test_taxonomy_prokka.nf.test.snap +++ b/tests/test_taxonomy_prokka.nf.test.snap @@ -24,14 +24,14 @@ }, "rgi": { "content": [ - "sample_1.txt:md5,fce130af51f93cccfc09ddaf9caf623f", - "sample_2.txt:md5,fce130af51f93cccfc09ddaf9caf623f" + "sample_1.txt:md5,601f0a16c0e999c2c5272d81f61bdf2f", + "sample_2.txt:md5,601f0a16c0e999c2c5272d81f61bdf2f" ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2024-07-24T13:05:30.025771" + "timestamp": "2025-09-04T13:50:43.240336665" }, "ampir": { "content": [ diff --git a/tests/test_taxonomy_pyrodigal.nf.test.snap b/tests/test_taxonomy_pyrodigal.nf.test.snap index b3d691bc..5e08d587 100644 --- a/tests/test_taxonomy_pyrodigal.nf.test.snap +++ b/tests/test_taxonomy_pyrodigal.nf.test.snap @@ -24,14 +24,14 @@ }, "rgi": { "content": [ - "sample_1.txt:md5,b7416895bc8ab11aea49cca8d6e1fe64", - "sample_2.txt:md5,b7416895bc8ab11aea49cca8d6e1fe64" + "sample_1.txt:md5,601f0a16c0e999c2c5272d81f61bdf2f", + "sample_2.txt:md5,601f0a16c0e999c2c5272d81f61bdf2f" ], "meta": { "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-07-08T17:09:16.360464299" + "timestamp": "2025-09-04T13:36:58.680604681" }, "ampir": { "content": [