From 85b12bcdd6a5fee149fe3d5e8262c05123e8eab7 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Sat, 17 Feb 2024 10:31:26 +1300 Subject: [PATCH] Now using a minimal bioconda recipe for ltr_finder_parallel (#4931) * Now using a minimal bioconda recipe for ltr_finder_parallel * Added missing tag --- modules/nf-core/ltrfinder/environment.yml | 2 +- modules/nf-core/ltrfinder/main.nf | 4 +- modules/nf-core/ltrfinder/tests/main.nf.test | 29 +++++--- .../nf-core/ltrfinder/tests/main.nf.test.snap | 68 ++++++++++++------- tests/config/test_data.config | 13 ++-- 5 files changed, 77 insertions(+), 39 deletions(-) diff --git a/modules/nf-core/ltrfinder/environment.yml b/modules/nf-core/ltrfinder/environment.yml index 289aadd3e93..7f3545975a8 100644 --- a/modules/nf-core/ltrfinder/environment.yml +++ b/modules/nf-core/ltrfinder/environment.yml @@ -6,4 +6,4 @@ channels: - bioconda - defaults dependencies: - - "bioconda::edta=2.2.0" + - "bioconda::ltr_finder_parallel=1.1" diff --git a/modules/nf-core/ltrfinder/main.nf b/modules/nf-core/ltrfinder/main.nf index 9573da55856..3e59e3c7acc 100644 --- a/modules/nf-core/ltrfinder/main.nf +++ b/modules/nf-core/ltrfinder/main.nf @@ -4,8 +4,8 @@ process LTRFINDER { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/edta:2.2.0--hdfd78af_1': - 'biocontainers/edta:2.2.0--hdfd78af_1' }" + 'https://depot.galaxyproject.org/singularity/ltr_finder_parallel:1.1--hdfd78af_0': + 'biocontainers/ltr_finder_parallel:1.1--hdfd78af_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/ltrfinder/tests/main.nf.test b/modules/nf-core/ltrfinder/tests/main.nf.test index a2eb9f6dd59..447ce34d3e1 100644 --- a/modules/nf-core/ltrfinder/tests/main.nf.test +++ b/modules/nf-core/ltrfinder/tests/main.nf.test @@ -7,16 +7,29 @@ nextflow_process { tag "modules" tag "modules_nfcore" tag "ltrfinder" + tag "gunzip/main" - test("homo_sapiens-genome_fasta-success") { + test("actinidia_chinensis-genome_21_fasta_gz-success") { + + setup { + run('GUNZIP') { + script "../../gunzip/main" + + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.test_data['actinidia_chinensis']['genome']['genome_21_fasta_gz'], checkIfExists: true) + ] + """ + } + } + } when { process { """ - input[0] = [ - [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - ] + input[0] = GUNZIP.out.gunzip """ } } @@ -25,7 +38,7 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot(process.out).match() }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(path(process.out.versions[0]).text).match("versions") } ) } @@ -40,7 +53,7 @@ nextflow_process { """ input[0] = [ [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + file(params.test_data['actinidia_chinensis']['genome']['genome_21_fasta_gz'], checkIfExists: true) ] """ } @@ -50,7 +63,7 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot(process.out).match() }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(path(process.out.versions[0]).text).match("stub_versions") } ) } diff --git a/modules/nf-core/ltrfinder/tests/main.nf.test.snap b/modules/nf-core/ltrfinder/tests/main.nf.test.snap index 547ca4856ef..54a2cee10f2 100644 --- a/modules/nf-core/ltrfinder/tests/main.nf.test.snap +++ b/modules/nf-core/ltrfinder/tests/main.nf.test.snap @@ -1,13 +1,5 @@ { - "versions": { - "content": [ - [ - "versions.yml:md5,2cff73621bfc5c4abc40613c33bd92b8" - ] - ], - "timestamp": "2023-12-05T09:09:31.335554" - }, - "stub": { + "actinidia_chinensis-genome_21_fasta_gz-success": { "content": [ { "0": [ @@ -15,7 +7,7 @@ { "id": "test" }, - "test.scn:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.scn:md5,006193c9eaf3f552ccb0369f159e7660" ] ], "1": [ @@ -23,18 +15,18 @@ { "id": "test" }, - "test.gff3:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.gff3:md5,96e5305163939e4381e1b94b660dc0a2" ] ], "2": [ - "versions.yml:md5,2cff73621bfc5c4abc40613c33bd92b8" + "versions.yml:md5,7b24225b810fa88cfb2a887de11be333" ], "gff": [ [ { "id": "test" }, - "test.gff3:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.gff3:md5,96e5305163939e4381e1b94b660dc0a2" ] ], "scn": [ @@ -42,17 +34,31 @@ { "id": "test" }, - "test.scn:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.scn:md5,006193c9eaf3f552ccb0369f159e7660" ] ], "versions": [ - "versions.yml:md5,2cff73621bfc5c4abc40613c33bd92b8" + "versions.yml:md5,7b24225b810fa88cfb2a887de11be333" ] } ], - "timestamp": "2024-01-16T10:01:22.368927" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-16T09:14:38.509965" }, - "homo_sapiens-genome_fasta-success": { + "versions": { + "content": [ + "\"LTRFINDER\":\n LTR_FINDER_parallel: v1.1\n ltr_finder: v1.07\n" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-16T09:16:55.301422" + }, + "stub": { "content": [ { "0": [ @@ -60,7 +66,7 @@ { "id": "test" }, - "test.scn:md5,2ce449dff751e59dbc292b6888491954" + "test.scn:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "1": [ @@ -68,18 +74,18 @@ { "id": "test" }, - "test.gff3:md5,a91c388a54d7694bd14a4b085935759c" + "test.gff3:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "2": [ - "versions.yml:md5,2cff73621bfc5c4abc40613c33bd92b8" + "versions.yml:md5,7b24225b810fa88cfb2a887de11be333" ], "gff": [ [ { "id": "test" }, - "test.gff3:md5,a91c388a54d7694bd14a4b085935759c" + "test.gff3:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "scn": [ @@ -87,14 +93,28 @@ { "id": "test" }, - "test.scn:md5,2ce449dff751e59dbc292b6888491954" + "test.scn:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "versions": [ - "versions.yml:md5,2cff73621bfc5c4abc40613c33bd92b8" + "versions.yml:md5,7b24225b810fa88cfb2a887de11be333" ] } ], - "timestamp": "2023-12-05T09:09:31.32397" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-16T09:14:43.054758" + }, + "stub_versions": { + "content": [ + "\"LTRFINDER\":\n LTR_FINDER_parallel: v1.1\n ltr_finder: v1.07\n" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-16T09:16:59.800724" } } \ No newline at end of file diff --git a/tests/config/test_data.config b/tests/config/test_data.config index dccf3e89bbd..676f4e2a4be 100644 --- a/tests/config/test_data.config +++ b/tests/config/test_data.config @@ -626,10 +626,15 @@ params { } 'saccharomyces_cerevisiae' { 'genome' { - samplesheet = "${params.test_data_base}/data/genomics/eukaryotes/saccharomyces_cerevisiae/samplesheet.csv" - genome_gfp_gtf = "${params.test_data_base}/data/genomics/eukaryotes/saccharomyces_cerevisiae/genome_gfp.gtf" - kallisto_results = "${params.test_data_base}/data/genomics/eukaryotes/saccharomyces_cerevisiae/kallisto_results.tar.gz" - salmon_results = "${params.test_data_base}/data/genomics/eukaryotes/saccharomyces_cerevisiae/salmon_results.tar.gz" + samplesheet = "${params.test_data_base}/data/genomics/eukaryotes/saccharomyces_cerevisiae/samplesheet.csv" + genome_gfp_gtf = "${params.test_data_base}/data/genomics/eukaryotes/saccharomyces_cerevisiae/genome_gfp.gtf" + kallisto_results = "${params.test_data_base}/data/genomics/eukaryotes/saccharomyces_cerevisiae/kallisto_results.tar.gz" + salmon_results = "${params.test_data_base}/data/genomics/eukaryotes/saccharomyces_cerevisiae/salmon_results.tar.gz" + } + } + 'actinidia_chinensis' { + 'genome' { + genome_21_fasta_gz = "${params.test_data_base}/data/genomics/eukaryotes/actinidia_chinensis/genome/chr1/genome.fasta.gz" } } 'generic' {