From 3d107f41baf68a8e8f4b5846f682f001f16af2b6 Mon Sep 17 00:00:00 2001 From: Thomas Krannich Date: Fri, 20 Dec 2024 11:21:13 +0100 Subject: [PATCH 1/2] initial commit of kma_index (#7236) * initial commit of kma_index * trying to fix linting for meta.yml * fix linting of meta.yml again * fixing DOI for linting * fixing file type for linting * fix output file name for linting * add snapshot * update output format * upgrade latest container build trying to satisfy docker CI --- modules/nf-core/kma/index/environment.yml | 7 ++ modules/nf-core/kma/index/main.nf | 52 +++++++++++ modules/nf-core/kma/index/meta.yml | 52 +++++++++++ modules/nf-core/kma/index/tests/main.nf.test | 59 ++++++++++++ .../nf-core/kma/index/tests/main.nf.test.snap | 92 +++++++++++++++++++ modules/nf-core/kma/index/tests/tags.yml | 2 + 6 files changed, 264 insertions(+) create mode 100644 modules/nf-core/kma/index/environment.yml create mode 100644 modules/nf-core/kma/index/main.nf create mode 100644 modules/nf-core/kma/index/meta.yml create mode 100644 modules/nf-core/kma/index/tests/main.nf.test create mode 100644 modules/nf-core/kma/index/tests/main.nf.test.snap create mode 100644 modules/nf-core/kma/index/tests/tags.yml diff --git a/modules/nf-core/kma/index/environment.yml b/modules/nf-core/kma/index/environment.yml new file mode 100644 index 00000000000..c8578084115 --- /dev/null +++ b/modules/nf-core/kma/index/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - bioconda + - conda-forge +dependencies: + - bioconda::kma=1.4.15 \ No newline at end of file diff --git a/modules/nf-core/kma/index/main.nf b/modules/nf-core/kma/index/main.nf new file mode 100644 index 00000000000..ebc700a997d --- /dev/null +++ b/modules/nf-core/kma/index/main.nf @@ -0,0 +1,52 @@ +process KMA_INDEX { + tag "$meta.id" + label 'process_low' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/kma:1.4.15--h577a1d6_1' : + 'biocontainers/kma:1.4.15--h577a1d6_1' }" + + input: + tuple val(meta), path(fasta) + + output: + tuple val(meta), path("kmaindex"), emit: index + path "versions.yml", emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def prefix = task.ext.prefix ?: "${fasta.baseName}" + def args = task.ext.args ?: '' + """ + mkdir kmaindex + kma \\ + index \\ + -i ${fasta} \\ + -o kmaindex/${prefix} \\ + $args + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + kma: \$(echo \$(kma_index -v 2>&1) | sed 's/^KMA_index-\$//') + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${fasta.baseName}" + """ + mkdir kmaindex + + touch kmaindex/${prefix}.comp.b + touch kmaindex/${prefix}.length.b + touch kmaindex/${prefix}.name + touch kmaindex/${prefix}.seq.b + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + kma: \$(echo \$(kma_index -v 2>&1) | sed 's/^KMA_index-\$//') + END_VERSIONS + """ +} diff --git a/modules/nf-core/kma/index/meta.yml b/modules/nf-core/kma/index/meta.yml new file mode 100644 index 00000000000..32f054a962e --- /dev/null +++ b/modules/nf-core/kma/index/meta.yml @@ -0,0 +1,52 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "kma_index" +description: This module wraps the index module of the KMA alignment tool. +keywords: + - alignment + - kma + - index + - database + - reads +tools: + - "kma": + description: "Rapid and precise alignment of raw reads against redundant databases with KMA" + homepage: "https://bitbucket.org/genomicepidemiology/kma/src/master/" + documentation: "https://bitbucket.org/genomicepidemiology/kma/src/master/" + tool_dev_url: "https://bitbucket.org/genomicepidemiology/kma/src/master/" + doi: "10.1186/s12859-018-2336-6" + licence: + ["http://www.apache.org/licenses/LICENSE-2.0"] + +input: + - - meta: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'reference' ]` + - fasta: + type: file + description: (Multi-)FASTA file of your database sequences. + pattern: "*.{fa,fasta}" + +output: + - index: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'reference' ]` + - 'kmaindex': + type: directory + description: Directory of KMA index files + pattern: "*.{comp.b,length.b,name,seq.b}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + +authors: + - "@krannich479" +maintainers: + - "@krannich479" diff --git a/modules/nf-core/kma/index/tests/main.nf.test b/modules/nf-core/kma/index/tests/main.nf.test new file mode 100644 index 00000000000..04054c1789b --- /dev/null +++ b/modules/nf-core/kma/index/tests/main.nf.test @@ -0,0 +1,59 @@ + +nextflow_process { + + name "Test Process KMA_INDEX" + script "../main.nf" + process "KMA_INDEX" + + tag "modules" + tag "modules_nfcore" + tag "kma" + tag "kma/index" + + test("sarscov2 - fasta") { + + when { + process { + """ + input[0] = [ + [ id:'MT192765.1', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - fasta - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'MT192765.1', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/kma/index/tests/main.nf.test.snap b/modules/nf-core/kma/index/tests/main.nf.test.snap new file mode 100644 index 00000000000..93c0510e8cc --- /dev/null +++ b/modules/nf-core/kma/index/tests/main.nf.test.snap @@ -0,0 +1,92 @@ +{ + "sarscov2 - fasta - stub": { + "content": [ + { + "0": [ + [ + { + "id": "MT192765.1", + "single_end": false + }, + [ + "genome.comp.b:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.length.b:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.name:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.seq.b:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "1": [ + "versions.yml:md5,ba9763933bdc811b1e19e466cceae9c8" + ], + "index": [ + [ + { + "id": "MT192765.1", + "single_end": false + }, + [ + "genome.comp.b:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.length.b:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.name:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.seq.b:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "versions": [ + "versions.yml:md5,ba9763933bdc811b1e19e466cceae9c8" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.3" + }, + "timestamp": "2024-12-19T17:07:30.875020727" + }, + "sarscov2 - fasta": { + "content": [ + { + "0": [ + [ + { + "id": "MT192765.1", + "single_end": false + }, + [ + "genome.comp.b:md5,2d4075cee26606cfb9b3624f8d7fe260", + "genome.length.b:md5,aaded6f5e19db3f3292e7ff9cd0157ec", + "genome.name:md5,e98cac0e614ac65bb458f77245af7d32", + "genome.seq.b:md5,48647a9697263fe218ddc728c2d01641" + ] + ] + ], + "1": [ + "versions.yml:md5,ba9763933bdc811b1e19e466cceae9c8" + ], + "index": [ + [ + { + "id": "MT192765.1", + "single_end": false + }, + [ + "genome.comp.b:md5,2d4075cee26606cfb9b3624f8d7fe260", + "genome.length.b:md5,aaded6f5e19db3f3292e7ff9cd0157ec", + "genome.name:md5,e98cac0e614ac65bb458f77245af7d32", + "genome.seq.b:md5,48647a9697263fe218ddc728c2d01641" + ] + ] + ], + "versions": [ + "versions.yml:md5,ba9763933bdc811b1e19e466cceae9c8" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.3" + }, + "timestamp": "2024-12-19T17:07:24.8942212" + } +} \ No newline at end of file diff --git a/modules/nf-core/kma/index/tests/tags.yml b/modules/nf-core/kma/index/tests/tags.yml new file mode 100644 index 00000000000..7e914abebfe --- /dev/null +++ b/modules/nf-core/kma/index/tests/tags.yml @@ -0,0 +1,2 @@ +kma/index: + - "modules/nf-core/kma/index/**" From 51c21921e151011213e5cf553cf06e6657e77594 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 20 Dec 2024 15:34:18 +0000 Subject: [PATCH 2/2] Refresh test snap for fastq_fastqc_umitools_fastp (#7256) --- .../tests/main.nf.test.snap | 870 +++++++++--------- 1 file changed, 435 insertions(+), 435 deletions(-) diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/main.nf.test.snap index bc9b84fc5cc..1addaba39ab 100644 --- a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/main.nf.test.snap @@ -28,7 +28,7 @@ "id": "test", "single_end": false }, - "test.fastp.json:md5,47a1bbd79b21721d81eb457e44fa3e3b" + "test.fastp.json:md5,1e0f8e27e71728e2b63fc64086be95cd" ] ], [ @@ -57,9 +57,9 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.2" + "nextflow": "24.10.3" }, - "timestamp": "2024-12-12T14:23:56.776685218" + "timestamp": "2024-12-20T14:49:55.964438399" }, "sarscov2 paired-end [fastq] | with_umi": { "content": [ @@ -87,7 +87,7 @@ "id": "test", "single_end": true }, - "test.fastp.json:md5,0ed43f6b2e5361e7ed6bc3c0b5d6e89a" + "test.fastp.json:md5,d39c5c6d9a2e35fb60d26ced46569af6" ] ], [ @@ -114,133 +114,11 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.2" - }, - "timestamp": "2024-12-12T14:23:44.160061128" - }, - "sarscov2 paired-end [fastq] | skip_trimming - stub": { - "content": [ - [ - - ], - [ - [ - { - "id": "test", - "single_end": false - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - [ - { - "id": "test", - "single_end": false - }, - "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - - ], - [ - - ], - [ - - ], - [ - - ], - [ - - ], - [ - - ], - [ - - ], - [ - - ], - [ - - ], - [ - "versions.yml:md5,f3dcaae948e8eed92b4a5557b4c6668e" - ] - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.2" + "nextflow": "24.10.3" }, - "timestamp": "2024-12-12T14:32:15.355312216" + "timestamp": "2024-12-20T14:49:32.102996566" }, - "sarscov2 paired-end [fastq] | umi_discard_read = 2": { - "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, - "unspecified" - ] - ], - [ - [ - { - "id": "test", - "single_end": false - }, - [ - "test_1.fastp.fastq.gz:md5,67b2bbae47f073e05a97a9c2edce23c7", - "test_2.fastp.fastq.gz:md5,25cbdca08e2083dbd4f0502de6b62f39" - ] - ] - ], - [ - [ - { - "id": "test", - "single_end": false - }, - "test.fastp.json:md5,47a1bbd79b21721d81eb457e44fa3e3b" - ] - ], - [ - [ - { - "id": "test", - "single_end": false - }, - 198 - ] - ], - [ - - ], - [ - - ], - [ - - ], - [ - "versions.yml:md5,85bd0117e5778fff18e3920972a296ad", - "versions.yml:md5,c50aa59475ab901bc6f9a2cf7b1a14e0", - "versions.yml:md5,f3dcaae948e8eed92b4a5557b4c6668e" - ] - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.2" - }, - "timestamp": "2024-12-12T14:24:09.203612468" - }, - "sarscov2 paired-end [fastq] | min_trimmed_reads = 26 - stub": { + "sarscov2 paired-end [fastq] | umi_discard_read = 2 - stub": { "content": [ { "0": [ @@ -270,7 +148,7 @@ "id": "test", "single_end": false }, - 26 + 1 ] ], "11": [ @@ -348,13 +226,7 @@ ], "9": [ - [ - { - "id": "test", - "single_end": false - }, - "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] + ], "adapter_seq": [ [ @@ -446,20 +318,14 @@ "id": "test", "single_end": false }, - 26 + 1 ] ], "trim_reads_fail": [ ], "trim_reads_merged": [ - [ - { - "id": "test", - "single_end": false - }, - "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] + ], "umi_log": [ @@ -475,9 +341,103 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, - "timestamp": "2024-12-12T14:32:39.987530839" + "timestamp": "2024-12-12T14:32:07.840128843" }, - "sarscov2 paired-end [fastq] | skip_fastqc": { + "sarscov2 paired-end [fastq] | skip_trimming - stub": { + "content": [ + [ + + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + + ], + [ + + ], + [ + + ], + [ + + ], + [ + + ], + [ + + ], + [ + + ], + [ + + ], + [ + + ], + [ + "versions.yml:md5,f3dcaae948e8eed92b4a5557b4c6668e" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.2" + }, + "timestamp": "2024-12-12T14:32:15.355312216" + }, + "sarscov2 paired-end [fastq] | skip_trimming": { + "content": [ + [ + + ], + { + "id": "test", + "single_end": false + }, + [ + + ], + [ + + ], + [ + + ], + [ + + ], + [ + + ], + [ + "versions.yml:md5,f3dcaae948e8eed92b4a5557b4c6668e" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.2" + }, + "timestamp": "2024-12-12T14:24:19.774510678" + }, + "sarscov2 paired-end [fastq] | umi_discard_read = 2": { "content": [ [ [ @@ -506,7 +466,7 @@ "id": "test", "single_end": false }, - "test.fastp.json:md5,47a1bbd79b21721d81eb457e44fa3e3b" + "test.fastp.json:md5,1e0f8e27e71728e2b63fc64086be95cd" ] ], [ @@ -528,16 +488,18 @@ ], [ - "versions.yml:md5,85bd0117e5778fff18e3920972a296ad" + "versions.yml:md5,85bd0117e5778fff18e3920972a296ad", + "versions.yml:md5,c50aa59475ab901bc6f9a2cf7b1a14e0", + "versions.yml:md5,f3dcaae948e8eed92b4a5557b4c6668e" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.2" + "nextflow": "24.10.3" }, - "timestamp": "2024-12-12T14:23:28.044081844" + "timestamp": "2024-12-20T14:50:21.346654157" }, - "sarscov2 paired-end [fastq] | skip_fastqc - stub": { + "sarscov2 paired-end [fastq] | min_trimmed_reads = 26 - stub": { "content": [ { "0": [ @@ -553,7 +515,13 @@ ] ], "1": [ - + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "10": [ [ @@ -561,20 +529,40 @@ "id": "test", "single_end": false }, - 1 + 26 ] ], "11": [ - + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "12": [ - 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