From c95215baf20e6d8cf2ae0e8411d03c5d9ef21d4a Mon Sep 17 00:00:00 2001 From: Mahesh Binzer-Panchal Date: Wed, 27 Mar 2024 05:50:31 +0100 Subject: [PATCH 1/4] Meryl count and meryl histogram migration to nf-test (#5401) * migrate to nf-test and update version * Add stub Co-authored-by: rodtheo * Fix linting Co-authored-by: rodtheo * Update test * Add kvalue as mandatory input * Add snapshot * Lint * Update GenomeScope2 module to reflect new mandatory parameter * migrate meryl/histogram to nf-test * Add mandatory kvalue to input * Lint Co-authored-by: rodtheo * Add stub Co-authored-by: rodtheo * Update test for meryl/histogram * Update meryl version * Remove meryl/histogram config and add input value to genomescope2 * Fix module path --------- Co-authored-by: rodtheo --- .../nf-core/genomescope2/tests/main.nf.test | 2 + .../genomescope2/tests/nextflow.config | 3 - modules/nf-core/meryl/count/environment.yml | 2 +- modules/nf-core/meryl/count/main.nf | 20 +- modules/nf-core/meryl/count/meta.yml | 6 +- .../nf-core/meryl/count/tests/main.nf.test | 60 ++++ .../meryl/count/tests/main.nf.test.snap | 332 ++++++++++++++++++ modules/nf-core/meryl/count/tests/tags.yml | 2 + .../nf-core/meryl/histogram/environment.yml | 2 +- modules/nf-core/meryl/histogram/main.nf | 18 +- modules/nf-core/meryl/histogram/meta.yml | 6 +- .../meryl/histogram/tests/main.nf.test | 70 ++++ .../meryl/histogram/tests/main.nf.test.snap | 72 ++++ .../nf-core/meryl/histogram/tests/tags.yml | 2 + tests/config/pytest_modules.yml | 6 - tests/modules/nf-core/meryl/count/main.nf | 28 -- .../nf-core/meryl/count/nextflow.config | 6 - tests/modules/nf-core/meryl/count/test.yml | 17 - tests/modules/nf-core/meryl/histogram/main.nf | 17 - .../nf-core/meryl/histogram/nextflow.config | 6 - .../modules/nf-core/meryl/histogram/test.yml | 10 - 21 files changed, 586 insertions(+), 101 deletions(-) create mode 100644 modules/nf-core/meryl/count/tests/main.nf.test create mode 100644 modules/nf-core/meryl/count/tests/main.nf.test.snap create mode 100644 modules/nf-core/meryl/count/tests/tags.yml create mode 100644 modules/nf-core/meryl/histogram/tests/main.nf.test create mode 100644 modules/nf-core/meryl/histogram/tests/main.nf.test.snap create mode 100644 modules/nf-core/meryl/histogram/tests/tags.yml delete mode 100644 tests/modules/nf-core/meryl/count/main.nf delete mode 100644 tests/modules/nf-core/meryl/count/nextflow.config delete mode 100644 tests/modules/nf-core/meryl/count/test.yml delete mode 100644 tests/modules/nf-core/meryl/histogram/main.nf delete mode 100644 tests/modules/nf-core/meryl/histogram/nextflow.config delete mode 100644 tests/modules/nf-core/meryl/histogram/test.yml diff --git a/modules/nf-core/genomescope2/tests/main.nf.test b/modules/nf-core/genomescope2/tests/main.nf.test index 677e4262a8a..20c74b328ad 100644 --- a/modules/nf-core/genomescope2/tests/main.nf.test +++ b/modules/nf-core/genomescope2/tests/main.nf.test @@ -20,6 +20,7 @@ nextflow_process { [ id: 'test', single_end: true ], // meta map file( params.modules_testdata_base_path + "/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_1.fastq.gz", checkIfExists: true ) ]) + input[1] = Channel.value(21) """ } } @@ -28,6 +29,7 @@ nextflow_process { process { """ input[0] = MERYL_COUNT.out.meryl_db + input[1] = Channel.value(21) """ } } diff --git a/modules/nf-core/genomescope2/tests/nextflow.config b/modules/nf-core/genomescope2/tests/nextflow.config index 33340158d60..6c6c2770e6e 100644 --- a/modules/nf-core/genomescope2/tests/nextflow.config +++ b/modules/nf-core/genomescope2/tests/nextflow.config @@ -1,7 +1,4 @@ process { - withName: 'MERYL.*' { - ext.args = 'k=21' - } withName: 'GENOMESCOPE2' { ext.args = '-k 21 -p 1 --fitted_hist' } diff --git a/modules/nf-core/meryl/count/environment.yml b/modules/nf-core/meryl/count/environment.yml index e2bac0f2ec1..808565ee796 100644 --- a/modules/nf-core/meryl/count/environment.yml +++ b/modules/nf-core/meryl/count/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::meryl=1.3 + - bioconda::meryl=1.4.1 diff --git a/modules/nf-core/meryl/count/main.nf b/modules/nf-core/meryl/count/main.nf index 073d11b63d1..2f0518f3ee9 100644 --- a/modules/nf-core/meryl/count/main.nf +++ b/modules/nf-core/meryl/count/main.nf @@ -4,11 +4,12 @@ process MERYL_COUNT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/meryl:1.3--h87f3376_1': - 'biocontainers/meryl:1.3--h87f3376_1' }" + 'https://depot.galaxyproject.org/singularity/meryl:1.4.1--h4ac6f70_0': + 'biocontainers/meryl:1.4.1--h4ac6f70_0' }" input: tuple val(meta), path(reads) + val kvalue output: tuple val(meta), path("*.meryldb"), emit: meryl_db @@ -23,6 +24,7 @@ process MERYL_COUNT { """ for READ in $reads; do meryl count \\ + k=$kvalue \\ threads=$task.cpus \\ $args \\ $reads \\ @@ -34,4 +36,18 @@ process MERYL_COUNT { meryl: \$( meryl --version |& sed 's/meryl //' ) END_VERSIONS """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + for READ in $reads; do + touch read.\${READ%.f*}.meryldb + done + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + meryl: \$( meryl --version |& sed 's/meryl //' ) + END_VERSIONS + """ } diff --git a/modules/nf-core/meryl/count/meta.yml b/modules/nf-core/meryl/count/meta.yml index a4de42e0bcc..c9347c0ca5d 100644 --- a/modules/nf-core/meryl/count/meta.yml +++ b/modules/nf-core/meryl/count/meta.yml @@ -3,13 +3,14 @@ description: A genomic k-mer counter (and sequence utility) with nice features. keywords: - k-mer - count + - reference-free tools: - "meryl": description: "A genomic k-mer counter (and sequence utility) with nice features. " homepage: "https://github.com/marbl/meryl" documentation: "https://meryl.readthedocs.io/en/latest/quick-start.html" tool_dev_url: "https://github.com/marbl/meryl" - licence: "['GPL']" + licence: ["GPL"] input: - meta: type: map @@ -21,6 +22,9 @@ input: description: | List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. + - kvalue: + type: integer + description: An integer value of k to use as the k-mer value. output: - meta: type: map diff --git a/modules/nf-core/meryl/count/tests/main.nf.test b/modules/nf-core/meryl/count/tests/main.nf.test new file mode 100644 index 00000000000..cce46c363e7 --- /dev/null +++ b/modules/nf-core/meryl/count/tests/main.nf.test @@ -0,0 +1,60 @@ +nextflow_process { + + name "Test Process MERYL_COUNT" + script "../main.nf" + process "MERYL_COUNT" + + tag "modules" + tag "modules_nfcore" + tag "meryl" + tag "meryl/count" + + test("bacteroides_fragilis - fastq") { + + when { + process { + """ + input[0] = Channel.value([ + [ id: 'test', single_end: true ], // meta map + file( params.modules_testdata_base_path + "/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_1.fastq.gz", checkIfExists: true ) + ]) + input[1] = Channel.value(21) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("bacteroides_fragilis - fastq - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.value([ + [ id: 'test', single_end: true ], // meta map + file( params.modules_testdata_base_path + "/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_1.fastq.gz", checkIfExists: true ) + ]) + input[1] = Channel.value(21) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/meryl/count/tests/main.nf.test.snap b/modules/nf-core/meryl/count/tests/main.nf.test.snap new file mode 100644 index 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"single_end": true + }, + "read.test1_1.meryldb:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,a4a6baac7481f1d4595ba54622bdf33d" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-26T19:30:13.745468405" + } +} \ No newline at end of file diff --git a/modules/nf-core/meryl/count/tests/tags.yml b/modules/nf-core/meryl/count/tests/tags.yml new file mode 100644 index 00000000000..b25bfa60655 --- /dev/null +++ b/modules/nf-core/meryl/count/tests/tags.yml @@ -0,0 +1,2 @@ +meryl/count: + - "modules/nf-core/meryl/count/**" diff --git a/modules/nf-core/meryl/histogram/environment.yml b/modules/nf-core/meryl/histogram/environment.yml index 4de66ee1a7c..09a324884da 100644 --- a/modules/nf-core/meryl/histogram/environment.yml +++ b/modules/nf-core/meryl/histogram/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::meryl=1.3 + - bioconda::meryl=1.4.1 diff --git a/modules/nf-core/meryl/histogram/main.nf b/modules/nf-core/meryl/histogram/main.nf index 32f1e9bbc54..622442cc671 100644 --- a/modules/nf-core/meryl/histogram/main.nf +++ b/modules/nf-core/meryl/histogram/main.nf @@ -4,11 +4,12 @@ process MERYL_HISTOGRAM { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/meryl:1.3--h87f3376_1': - 'biocontainers/meryl:1.3--h87f3376_1' }" + 'https://depot.galaxyproject.org/singularity/meryl:1.4.1--h4ac6f70_0': + 'biocontainers/meryl:1.4.1--h4ac6f70_0' }" input: tuple val(meta), path(meryl_db) + val kvalue output: tuple val(meta), path("*.hist"), emit: hist @@ -22,6 +23,7 @@ process MERYL_HISTOGRAM { def prefix = task.ext.prefix ?: "${meta.id}" """ meryl histogram \\ + k=$kvalue \\ threads=$task.cpus \\ $args \\ $meryl_db > ${prefix}.hist @@ -31,4 +33,16 @@ process MERYL_HISTOGRAM { meryl: \$( meryl --version |& sed 's/meryl //' ) END_VERSIONS """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.hist + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + meryl: \$( meryl --version |& sed 's/meryl //' ) + END_VERSIONS + """ } diff --git a/modules/nf-core/meryl/histogram/meta.yml b/modules/nf-core/meryl/histogram/meta.yml index f8d2b43f9c0..fb67f4ef05e 100644 --- a/modules/nf-core/meryl/histogram/meta.yml +++ b/modules/nf-core/meryl/histogram/meta.yml @@ -3,13 +3,14 @@ description: A genomic k-mer counter (and sequence utility) with nice features. keywords: - k-mer - histogram + - reference-free tools: - "meryl": description: "A genomic k-mer counter (and sequence utility) with nice features. " homepage: "https://github.com/marbl/meryl" documentation: "https://meryl.readthedocs.io/en/latest/quick-start.html" tool_dev_url: "https://github.com/marbl/meryl" - licence: "['GPL']" + licence: ["GPL"] input: - meta: type: map @@ -19,6 +20,9 @@ input: - meryl_dbs: type: directory description: Meryl k-mer database + - kvalue: + type: integer + description: An integer value of k to use as the k-mer value. output: - meta: type: map diff --git a/modules/nf-core/meryl/histogram/tests/main.nf.test b/modules/nf-core/meryl/histogram/tests/main.nf.test new file mode 100644 index 00000000000..307fa39b4a5 --- /dev/null +++ b/modules/nf-core/meryl/histogram/tests/main.nf.test @@ -0,0 +1,70 @@ +nextflow_process { + + name "Test Process MERYL_HISTOGRAM" + script "../main.nf" + process "MERYL_HISTOGRAM" + + tag "modules" + tag "modules_nfcore" + tag "meryl" + tag "meryl/count" + tag "meryl/histogram" + + setup { + run('MERYL_COUNT'){ + script "../../../../../modules/nf-core/meryl/count/main.nf" + process { + """ + input[0] = Channel.value([ + [ id: 'test', single_end: true ], // meta map + file( params.modules_testdata_base_path + "/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_1.fastq.gz", checkIfExists: true ) + ]) + input[1] = Channel.value(21) + """ + } + } + } + + test("bacteroides_fragilis - fastq") { + + when { + process { + """ + input[0] = MERYL_COUNT.out.meryl_db + input[1] = Channel.value(21) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("bacteroides_fragilis - fastq - stub") { + + options "-stub" + + when { + process { + """ + input[0] = MERYL_COUNT.out.meryl_db + input[1] = Channel.value(21) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/meryl/histogram/tests/main.nf.test.snap b/modules/nf-core/meryl/histogram/tests/main.nf.test.snap new file mode 100644 index 00000000000..7b2c239e5da --- /dev/null +++ b/modules/nf-core/meryl/histogram/tests/main.nf.test.snap @@ -0,0 +1,72 @@ +{ + "bacteroides_fragilis - fastq": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.hist:md5,f75362ab9cd70d96621b3690e952085f" + ] + ], + "1": [ + "versions.yml:md5,6f83b51cf2e3bc82d1a9823cacf220a5" + ], + "hist": [ + [ + { + "id": "test", + "single_end": true + }, + "test.hist:md5,f75362ab9cd70d96621b3690e952085f" + ] + ], + "versions": [ + "versions.yml:md5,6f83b51cf2e3bc82d1a9823cacf220a5" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-26T20:30:27.901802038" + }, + "bacteroides_fragilis - fastq - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.hist:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,6f83b51cf2e3bc82d1a9823cacf220a5" + ], + "hist": [ + [ + { + "id": "test", + "single_end": true + }, + "test.hist:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,6f83b51cf2e3bc82d1a9823cacf220a5" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-26T20:30:46.254942627" + } +} \ No newline at end of file diff --git a/modules/nf-core/meryl/histogram/tests/tags.yml b/modules/nf-core/meryl/histogram/tests/tags.yml new file mode 100644 index 00000000000..39fbc344201 --- /dev/null +++ b/modules/nf-core/meryl/histogram/tests/tags.yml @@ -0,0 +1,2 @@ +meryl/histogram: + - "modules/nf-core/meryl/histogram/**" diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index a539e80802b..f4ff16b7156 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -1234,12 +1234,6 @@ merquryfk/merquryfk: merquryfk/ploidyplot: - modules/nf-core/merquryfk/ploidyplot/** - tests/modules/nf-core/merquryfk/ploidyplot/** -meryl/count: - - modules/nf-core/meryl/count/** - - tests/modules/nf-core/meryl/count/** -meryl/histogram: - - modules/nf-core/meryl/histogram/** - - tests/modules/nf-core/meryl/histogram/** meryl/unionsum: - modules/nf-core/meryl/unionsum/** - tests/modules/nf-core/meryl/unionsum/** diff --git a/tests/modules/nf-core/meryl/count/main.nf b/tests/modules/nf-core/meryl/count/main.nf deleted file mode 100644 index cd71fb983da..00000000000 --- a/tests/modules/nf-core/meryl/count/main.nf +++ /dev/null @@ -1,28 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { MERYL_COUNT } from '../../../../../modules/nf-core/meryl/count/main.nf' - -workflow test_meryl_count_single_end { - - input = [ - [ id:'test' , single_end: true ], // meta map - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) - ] - - MERYL_COUNT ( input ) -} - -workflow test_meryl_count_paired_end { - - input = [ - [ id:'test' , single_end: false ], // meta map - [ - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) - ] - ] - - MERYL_COUNT ( input ) -} diff --git a/tests/modules/nf-core/meryl/count/nextflow.config b/tests/modules/nf-core/meryl/count/nextflow.config deleted file mode 100644 index 6d899c503af..00000000000 --- a/tests/modules/nf-core/meryl/count/nextflow.config +++ /dev/null @@ -1,6 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - ext.args = 'k=21' - -} diff --git a/tests/modules/nf-core/meryl/count/test.yml b/tests/modules/nf-core/meryl/count/test.yml deleted file mode 100644 index 7f4f9a50aac..00000000000 --- a/tests/modules/nf-core/meryl/count/test.yml +++ /dev/null @@ -1,17 +0,0 @@ -- name: meryl count test_meryl_count_single_end - command: nextflow run ./tests/modules/nf-core/meryl/count -entry test_meryl_count_single_end -c ./tests/config/nextflow.config - tags: - - meryl/count - - meryl - files: - - path: output/meryl/versions.yml - md5sum: 5fe537d873925ccbcc4edf0983e9eda0 - -- name: meryl count test_meryl_count_paired_end - command: nextflow run ./tests/modules/nf-core/meryl/count -entry test_meryl_count_paired_end -c ./tests/config/nextflow.config - tags: - - meryl/count - - meryl - files: - - path: output/meryl/versions.yml - md5sum: 4961f13cfb60ba8764ed666e70dbf12c diff --git a/tests/modules/nf-core/meryl/histogram/main.nf b/tests/modules/nf-core/meryl/histogram/main.nf deleted file mode 100644 index 153a76d44bf..00000000000 --- a/tests/modules/nf-core/meryl/histogram/main.nf +++ /dev/null @@ -1,17 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { MERYL_COUNT } from '../../../../../modules/nf-core/meryl/count/main.nf' -include { MERYL_HISTOGRAM } from '../../../../../modules/nf-core/meryl/histogram/main.nf' - -workflow test_meryl_histogram { - - input = [ - [ id:'test' ], // meta map - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) - ] - - MERYL_COUNT ( input ) - MERYL_HISTOGRAM ( MERYL_COUNT.out.meryl_db ) -} diff --git a/tests/modules/nf-core/meryl/histogram/nextflow.config b/tests/modules/nf-core/meryl/histogram/nextflow.config deleted file mode 100644 index 6d899c503af..00000000000 --- a/tests/modules/nf-core/meryl/histogram/nextflow.config +++ /dev/null @@ -1,6 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - ext.args = 'k=21' - -} diff --git a/tests/modules/nf-core/meryl/histogram/test.yml b/tests/modules/nf-core/meryl/histogram/test.yml deleted file mode 100644 index 7d794aa773b..00000000000 --- a/tests/modules/nf-core/meryl/histogram/test.yml +++ /dev/null @@ -1,10 +0,0 @@ -- name: meryl histogram test_meryl_histogram - command: nextflow run ./tests/modules/nf-core/meryl/histogram -entry test_meryl_histogram -c ./tests/config/nextflow.config - tags: - - meryl/histogram - - meryl - files: - - path: output/meryl/test.hist - md5sum: 4bfdc8b287ee0cfd9922bbfa8cd64650 - - path: output/meryl/versions.yml - md5sum: 050038f1b1df79977a393cce1b4b2ddb From 5f2f5ca857c25f794f69c8127a6d9a3a592ab857 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luc=C3=ADa=20Pe=C3=B1a-P=C3=A9rez?= Date: Wed, 27 Mar 2024 10:32:06 +0100 Subject: [PATCH 2/4] corrected bug in asereadcounter (#5403) * feat corrected bug * Update modules/nf-core/gatk4/asereadcounter/main.nf Co-authored-by: James A. Fellows Yates --------- Co-authored-by: lucia.pena.perez@scilifelab.se Co-authored-by: James A. Fellows Yates --- modules/nf-core/gatk4/asereadcounter/main.nf | 11 +++++------ modules/nf-core/gatk4/asereadcounter/main.nf.test | 13 +++++-------- modules/nf-core/gatk4/asereadcounter/meta.yml | 11 +++-------- 3 files changed, 13 insertions(+), 22 deletions(-) diff --git a/modules/nf-core/gatk4/asereadcounter/main.nf b/modules/nf-core/gatk4/asereadcounter/main.nf index 9b5b62a2061..cb9083e0761 100644 --- a/modules/nf-core/gatk4/asereadcounter/main.nf +++ b/modules/nf-core/gatk4/asereadcounter/main.nf @@ -8,11 +8,10 @@ process GATK4_ASEREADCOUNTER { 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" input: - tuple val(meta), path(input), path(input_index) - tuple val(meta2), path(vcf), path(tbi) - tuple val(meta3), path(fasta) - tuple val(meta4), path(fai) - tuple val(meta5), path(dict) + tuple val(meta), path(bam), path(bai), path(vcf), path(tbi) + tuple val(meta2), path(fasta) + tuple val(meta3), path(fai) + tuple val(meta4), path(dict) path intervals output: @@ -39,7 +38,7 @@ process GATK4_ASEREADCOUNTER { gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\ ASEReadCounter \\ --output ${prefix}_ase.csv \\ - --input ${input} \\ + --input ${bam} \\ --variant ${vcf} \\ $reference_command \\ $intervals_command \\ diff --git a/modules/nf-core/gatk4/asereadcounter/main.nf.test b/modules/nf-core/gatk4/asereadcounter/main.nf.test index e532d38d9af..9f80708f01e 100644 --- a/modules/nf-core/gatk4/asereadcounter/main.nf.test +++ b/modules/nf-core/gatk4/asereadcounter/main.nf.test @@ -16,26 +16,23 @@ nextflow_process { input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path +'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path +'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) - ] - input[1] = [ - [ id:'test' ], // meta map + file(params.modules_testdata_base_path +'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), file(params.modules_testdata_base_path +'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path +'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) ] - input[2] = [ + input[1] = [ [ id:'reference' ], // meta map file(params.modules_testdata_base_path +'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] - input[3] = [ + input[2] = [ [ id:'reference' ], // meta map file(params.modules_testdata_base_path +'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] - input[4] = [ + input[3] = [ [ id:'reference' ], // meta map file(params.modules_testdata_base_path +'genomics/sarscov2/genome/genome.dict', checkIfExists: true) ] - input[5] = [ + input[4] = [ file(params.modules_testdata_base_path +'genomics/sarscov2/genome/picard/targets.interval_list', checkIfExists: true) ] """ diff --git a/modules/nf-core/gatk4/asereadcounter/meta.yml b/modules/nf-core/gatk4/asereadcounter/meta.yml index 7367dec7eca..1adfaa813ae 100644 --- a/modules/nf-core/gatk4/asereadcounter/meta.yml +++ b/modules/nf-core/gatk4/asereadcounter/meta.yml @@ -29,11 +29,6 @@ input: type: file description: index file for input file pattern: "*.{bai,crai}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'reference' ]` - vcf: type: file description: VCF file @@ -42,7 +37,7 @@ input: type: file description: index file for VCF file pattern: "*.{vcf.gz.tbi}" - - meta3: + - meta2: type: map description: | Groovy Map containing reference information @@ -51,7 +46,7 @@ input: type: file description: fasta file pattern: "*.{fasta,fa}" - - meta4: + - meta3: type: map description: | Groovy Map containing reference information @@ -60,7 +55,7 @@ input: type: file description: fasta index file pattern: "*.{fai}" - - meta5: + - meta4: type: map description: | Groovy Map containing reference information From a3501bcf46d42ed9d4174bbc132c7505dc62b4b3 Mon Sep 17 00:00:00 2001 From: DavideBag <96130443+DavideBag@users.noreply.github.com> Date: Wed, 27 Mar 2024 12:32:00 +0100 Subject: [PATCH 3/4] Adding Fast epistasis module (#5389) * adding fastepistasis module * fixing version in main test * Update modules/nf-core/plink/fastepistasis/main.nf Co-authored-by: Francesco Lescai <53608000+lescai@users.noreply.github.com> --------- Co-authored-by: Francesco Lescai <53608000+lescai@users.noreply.github.com> --- .../plink/fastepistasis/environment.yml | 9 + modules/nf-core/plink/fastepistasis/main.nf | 94 +++++++++ modules/nf-core/plink/fastepistasis/meta.yml | 97 +++++++++ .../plink/fastepistasis/tests/main.nf.test | 190 ++++++++++++++++++ .../fastepistasis/tests/main.nf.test.snap | 170 ++++++++++++++++ .../plink/fastepistasis/tests/nextflow.config | 7 + .../fastepistasis/tests/pheno_name.config | 7 + .../plink/fastepistasis/tests/tags.yml | 2 + 8 files changed, 576 insertions(+) create mode 100644 modules/nf-core/plink/fastepistasis/environment.yml create mode 100644 modules/nf-core/plink/fastepistasis/main.nf create mode 100644 modules/nf-core/plink/fastepistasis/meta.yml create mode 100644 modules/nf-core/plink/fastepistasis/tests/main.nf.test create mode 100644 modules/nf-core/plink/fastepistasis/tests/main.nf.test.snap create mode 100644 modules/nf-core/plink/fastepistasis/tests/nextflow.config create mode 100644 modules/nf-core/plink/fastepistasis/tests/pheno_name.config create mode 100644 modules/nf-core/plink/fastepistasis/tests/tags.yml diff --git a/modules/nf-core/plink/fastepistasis/environment.yml b/modules/nf-core/plink/fastepistasis/environment.yml new file mode 100644 index 00000000000..6bd1701d725 --- /dev/null +++ b/modules/nf-core/plink/fastepistasis/environment.yml @@ -0,0 +1,9 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +name: "plink_fastepistasis" +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - "bioconda::plink=1.90b6.21" diff --git a/modules/nf-core/plink/fastepistasis/main.nf b/modules/nf-core/plink/fastepistasis/main.nf new file mode 100644 index 00000000000..8bdd30b1322 --- /dev/null +++ b/modules/nf-core/plink/fastepistasis/main.nf @@ -0,0 +1,94 @@ +process PLINK_FASTEPISTASIS { + tag "$meta.id" + label 'process_low' + + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/plink:1.90b6.21--h031d066_5': + 'biocontainers/plink:1.90b6.21--h031d066_5' }" + + input: + tuple val(meta), path(bed), path(bim), path(fam) + tuple val(meta2), path(vcf) + tuple val(meta3), path(bcf) + tuple val(meta4), path(phe) + + output: + tuple val(meta), path("*.epi.cc") , emit: fepi + tuple val(meta), path("*.epi.cc.summary"), emit: fepisummary, optional:true + tuple val(meta), path("*.log") , emit: flog + tuple val(meta), path("*.nosex") , emit: fnosex, optional:true + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = "" + // define input string based on provided input files + // in hierarchical order + def input_command = "" + def outmeta = "" + if (bed){ + input_command = "--bed ${bed} --bim ${bim} --fam ${fam}" + prefix = task.ext.prefix ?: "${meta.id}" + } else if (vcf) { + input_command = "--vcf ${vcf} --pheno ${phe}" + prefix = task.ext.prefix ?: "${meta2.id}" + meta = meta2 + } else if (bcf) { + input_command = "--bcf ${bcf} --pheno ${phe}" + prefix = task.ext.prefix ?: "${meta3.id}" + meta = meta3 + } else { + log.error 'ERROR: the input should be either plink native binary format, VCF or BCF' + } + """ + plink \\ + $input_command \\ + --threads $task.cpus \\ + --fast-epistasis \\ + $args \\ + --out $prefix + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + plink: \$(samtools --version |& sed '1!d ; s/samtools //') + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def prefix = "" + // define input string based on provided input files + // in hierarchical order + def input_command = "" + def outmeta = "" + if (bed){ + input_command = "--bed ${bed} --bim ${bim} --fam ${fam}" + prefix = task.ext.prefix ?: "${meta.id}" + } else if (vcf) { + input_command = "--vcf ${vcf}" + prefix = task.ext.prefix ?: "${meta2.id} --pheno ${pheno}" + meta = meta2 + } else if (bcf) { + input_command = "--bcf ${bcf} --pheno ${pheno}" + prefix = task.ext.prefix ?: "${meta3.id}" + meta = meta3 + } else { + log.error 'ERROR: the input should be either plink native binary format, VCF or BCF' + } + """ + touch ${prefix}.fepi + touch ${prefix}.fepisummary + touch ${prefix}.flog + touch ${prefix}.fnosex + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + plink: \$(echo \$(plink --version) | sed 's/^PLINK v//;s/64.*//') + END_VERSIONS + """ +} diff --git a/modules/nf-core/plink/fastepistasis/meta.yml b/modules/nf-core/plink/fastepistasis/meta.yml new file mode 100644 index 00000000000..0545c66dd61 --- /dev/null +++ b/modules/nf-core/plink/fastepistasis/meta.yml @@ -0,0 +1,97 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "plink_fastepistasis" +description: Fast Epistasis in PLINK, analyzing how the effects of one gene depend on the presence of others. +keywords: + - interactions + - variants + - regression +tools: + - "plink": + description: "Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner." + homepage: "https://www.cog-genomics.org/plink" + documentation: "https://www.cog-genomics.org/plink/1.9/data#recode" + tool_dev_url: "https://www.cog-genomics.org/plink/1.9/dev" + licence: ["GPL"] + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + meta is associated to the PLINK native file input + - meta2: + type: map + description: | + Groovy Map containing sample information, + e.g. [ id:'test', single_end:false ] + meta2 is associated to VCF file input + - meta3: + type: map + description: | + Groovy Map containing sample information, + e.g. [ id:'test', single_end:false ] + meta3 is associated to BCF file input + - meta4: + type: map + description: | + Groovy Map containing sample information, + e.g. [ id:'test', single_end:false ] + meta4 is associated to phenotype file input + - bed: + type: file + description: PLINK binary biallelic genotype table file + pattern: "*.{bed}" + - bim: + type: file + description: PLINK extended MAP file + pattern: "*.{bim}" + - fam: + type: file + description: PLINK sample information file + pattern: "*.{fam}" + - bcf: + type: file + description: PLINK variant information + sample ID + genotype call binary file + pattern: "*.{bcf}" + - vcf: + type: file + description: Variant calling file (vcf) + pattern: "*.{vcf}" + - phe: + type: file + description: PLINK file containing phenotype information. This phenotype information can be read from the third column with the --pheno option or from a specific column with the --pheno-name option. + pattern: "*.{phe}" + +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - fepi: + type: file + description: PLINK fast-epistasis file + pattern: "*.{epi.cc}" + - fepisummary: + type: file + description: PLINK fast-epistasis summary file + pattern: "*.{epi.cc.summary}" + - flog: + type: file + description: PLINK fast-epistasis log file + pattern: "*.{log}" + - fnosex: + type: file + description: Ambiguous sex ID file + pattern: "*.{nosex}" + +authors: + - "@davidebag" +maintainers: + - "@davidebag" diff --git a/modules/nf-core/plink/fastepistasis/tests/main.nf.test b/modules/nf-core/plink/fastepistasis/tests/main.nf.test new file mode 100644 index 00000000000..ac234c4b494 --- /dev/null +++ b/modules/nf-core/plink/fastepistasis/tests/main.nf.test @@ -0,0 +1,190 @@ +nextflow_process { + + name "Test Process PLINK_FASTEPISTASIS" + script "../main.nf" + process "PLINK_FASTEPISTASIS" + tag "modules" + tag "modules_nfcore" + tag "plink" + tag "plink/fastepistasis" + + test("plink - VCF") { + + config "./nextflow.config" + + when { + params { + outdir = "test" + } + process { + """ + input[0] = [ [id:"null"], [], [], []] + input[1] = [ + [id:"test"], + file(params.test_data['homo_sapiens']['popgen']['plink_case_control_vcf_gz'], checkIfExists: true) + ] + input[2] = [ [id:"null"], []] + input[3] = [ + [id:"test"], + file(params.test_data['homo_sapiens']['popgen']['plink_simulated_phe'], checkIfExists: true) + ] + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.version).match("version") }, + { assert snapshot( + process.out.fepi, + process.out.fepisummary, + process.out.fnosex + ).match() }, + { assert process.out.flog.get(0).get(1) ==~ ".*/*.log" } + ) + } + } + + test("plink - VCF with phenotype name") { + + config "./pheno_name.config" + + when { + params { + outdir = "test" + } + process { + """ + input[0] = [ [id:"null"], [], [], []] + input[1] = [ + [id:"test"], + file(params.test_data['homo_sapiens']['popgen']['plink_case_control_vcf_gz'], checkIfExists: true) + ] + input[2] = [ [id:"null"], []] + input[3] = [ + [id:"test"], + file(params.test_data['homo_sapiens']['popgen']['plink_simulated_phenoname'], checkIfExists: true) + ] + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.fepi, + process.out.fepisummary, + process.out.fnosex + ).match() }, + { assert process.out.flog.get(0).get(1) ==~ ".*/*.log" } + ) + } + } + + test("plink - binary") { + + config "./nextflow.config" + + when { + params { + outdir = "test" + } + process { + """ + input[0] = [ + [id:"test"], + file(params.test_data['homo_sapiens']['popgen']['plink_case_control_bed'], checkIfExists: true), + file(params.test_data['homo_sapiens']['popgen']['plink_case_control_bim'], checkIfExists: true), + file(params.test_data['homo_sapiens']['popgen']['plink_case_control_fam'], checkIfExists: true) + ] + input[1] = [ [id:"null"], []] + input[2] = [ [id:"null"], []] + input[3] = [ [id:"null"], []] + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.fepi, + process.out.fepisummary, + process.out.fnosex + ).match() }, + { assert process.out.flog.get(0).get(1) ==~ ".*/*.log" } + ) + } + } + + test("plink - BCF") { + + config "./nextflow.config" + + when { + params { + outdir = "test" + } + process { + """ + input[0] = [ [id:"null"], [], [], []] + input[1] = [ [id:"null"], []] + input[2] = [ + [id:"test"], + file(params.test_data['homo_sapiens']['popgen']['plink_case_control_bcf_gz'], checkIfExists: true) + ] + input[3] = [ + [id:"test"], + file(params.test_data['homo_sapiens']['popgen']['plink_simulated_phe'], checkIfExists: true) + ] + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.fepi, + process.out.fepisummary, + process.out.fnosex + ).match() }, + { assert process.out.flog.get(0).get(1) ==~ ".*/*.log" } + ) + } + } + + test("plink - BCF with phenotype name") { + + config "./pheno_name.config" + + when { + params { + outdir = "test" + } + process { + """ + input[0] = [ [id:"null"], [], [], []] + input[1] = [ + [id:"test"], + file(params.test_data['homo_sapiens']['popgen']['plink_case_control_vcf_gz'], checkIfExists: true) + ] + input[2] = [ [id:"null"], []] + input[3] = [ + [id:"test"], + file(params.test_data['homo_sapiens']['popgen']['plink_simulated_phenoname'], checkIfExists: true) + ] + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.fepi, + process.out.fepisummary, + process.out.fnosex + ).match() }, + { assert process.out.flog.get(0).get(1) ==~ ".*/*.log" } + ) + } + } +} \ No newline at end of file diff --git a/modules/nf-core/plink/fastepistasis/tests/main.nf.test.snap b/modules/nf-core/plink/fastepistasis/tests/main.nf.test.snap new file mode 100644 index 00000000000..919ae910d2c --- /dev/null +++ b/modules/nf-core/plink/fastepistasis/tests/main.nf.test.snap @@ -0,0 +1,170 @@ +{ + "plink - BCF": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.epi.cc:md5,5be26940bec7ce556da4062c974e6605" + ] + ], + [ + [ + { + "id": "test" + }, + "test.epi.cc.summary:md5,e955ebbfc5b5bcb7f37dbaa8b5ed7196" + ] + ], + [ + [ + { + "id": "test" + }, + "test.nosex:md5,4f9aa36c44a417ff6d7caa9841e66ad9" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-25T15:54:18.804673977" + }, + "plink - BCF with phenotype name": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.epi.cc:md5,5be26940bec7ce556da4062c974e6605" + ] + ], + [ + [ + { + "id": "test" + }, + "test.epi.cc.summary:md5,e955ebbfc5b5bcb7f37dbaa8b5ed7196" + ] + ], + [ + [ + { + "id": "test" + }, + "test.nosex:md5,4f9aa36c44a417ff6d7caa9841e66ad9" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-25T15:54:28.893162946" + }, + "plink - VCF with phenotype name": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.epi.cc:md5,5be26940bec7ce556da4062c974e6605" + ] + ], + [ + [ + { + "id": "test" + }, + "test.epi.cc.summary:md5,e955ebbfc5b5bcb7f37dbaa8b5ed7196" + ] + ], + [ + [ + { + "id": "test" + }, + "test.nosex:md5,4f9aa36c44a417ff6d7caa9841e66ad9" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-25T15:53:56.070572393" + }, + "plink - binary": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.epi.cc:md5,5be26940bec7ce556da4062c974e6605" + ] + ], + [ + [ + { + "id": "test" + }, + "test.epi.cc.summary:md5,e955ebbfc5b5bcb7f37dbaa8b5ed7196" + ] + ], + [ + + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-25T15:54:08.487963135" + }, + "plink - VCF": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.epi.cc:md5,5be26940bec7ce556da4062c974e6605" + ] + ], + [ + [ + { + "id": "test" + }, + "test.epi.cc.summary:md5,e955ebbfc5b5bcb7f37dbaa8b5ed7196" + ] + ], + [ + [ + { + "id": "test" + }, + "test.nosex:md5,4f9aa36c44a417ff6d7caa9841e66ad9" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-25T15:53:44.711384951" + }, + "version": { + "content": null, + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-25T15:53:44.699910482" + } +} \ No newline at end of file diff --git a/modules/nf-core/plink/fastepistasis/tests/nextflow.config b/modules/nf-core/plink/fastepistasis/tests/nextflow.config new file mode 100644 index 00000000000..72d38d17084 --- /dev/null +++ b/modules/nf-core/plink/fastepistasis/tests/nextflow.config @@ -0,0 +1,7 @@ +process { + + withName: PLINK_FASTEPISTASIS { + ext.args = '--allow-no-sex' + } + +} diff --git a/modules/nf-core/plink/fastepistasis/tests/pheno_name.config b/modules/nf-core/plink/fastepistasis/tests/pheno_name.config new file mode 100644 index 00000000000..86da841c30e --- /dev/null +++ b/modules/nf-core/plink/fastepistasis/tests/pheno_name.config @@ -0,0 +1,7 @@ +process { + + withName: PLINK_FASTEPISTASIS { + ext.args = '--pheno-name Phenotype --allow-no-sex' + } + +} diff --git a/modules/nf-core/plink/fastepistasis/tests/tags.yml b/modules/nf-core/plink/fastepistasis/tests/tags.yml new file mode 100644 index 00000000000..f946dcc4c99 --- /dev/null +++ b/modules/nf-core/plink/fastepistasis/tests/tags.yml @@ -0,0 +1,2 @@ +plink/fastepistasis: + - "modules/nf-core/plink/fastepistasis/**" From b7f584e61c35c138a5717f837f4da9b838e290a7 Mon Sep 17 00:00:00 2001 From: Mahesh Binzer-Panchal Date: Wed, 27 Mar 2024 12:45:03 +0100 Subject: [PATCH 4/4] Migrate meryl unionsum nftest (#5404) * Initial migration * Update tests, add mandatory value, lint * Bump version * Update snapshot --- .../nf-core/meryl/unionsum/environment.yml | 2 +- modules/nf-core/meryl/unionsum/main.nf | 18 +- modules/nf-core/meryl/unionsum/meta.yml | 6 +- .../nf-core/meryl/unionsum/tests/main.nf.test | 123 ++++ .../meryl/unionsum/tests/main.nf.test.snap | 627 ++++++++++++++++++ modules/nf-core/meryl/unionsum/tests/tags.yml | 2 + tests/config/pytest_modules.yml | 3 - tests/modules/nf-core/meryl/unionsum/main.nf | 31 - .../nf-core/meryl/unionsum/nextflow.config | 6 - tests/modules/nf-core/meryl/unionsum/test.yml | 17 - 10 files changed, 774 insertions(+), 61 deletions(-) create mode 100644 modules/nf-core/meryl/unionsum/tests/main.nf.test create mode 100644 modules/nf-core/meryl/unionsum/tests/main.nf.test.snap create mode 100644 modules/nf-core/meryl/unionsum/tests/tags.yml delete mode 100644 tests/modules/nf-core/meryl/unionsum/main.nf delete mode 100644 tests/modules/nf-core/meryl/unionsum/nextflow.config delete mode 100644 tests/modules/nf-core/meryl/unionsum/test.yml diff --git a/modules/nf-core/meryl/unionsum/environment.yml b/modules/nf-core/meryl/unionsum/environment.yml index 5ff25fed86b..b8bdcbe8767 100644 --- a/modules/nf-core/meryl/unionsum/environment.yml +++ b/modules/nf-core/meryl/unionsum/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::meryl=1.3 + - bioconda::meryl=1.4.1 diff --git a/modules/nf-core/meryl/unionsum/main.nf b/modules/nf-core/meryl/unionsum/main.nf index 541c9e18a1a..3ee86e0f3bb 100644 --- a/modules/nf-core/meryl/unionsum/main.nf +++ b/modules/nf-core/meryl/unionsum/main.nf @@ -4,11 +4,12 @@ process MERYL_UNIONSUM { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/meryl:1.3--h87f3376_1': - 'biocontainers/meryl:1.3--h87f3376_1' }" + 'https://depot.galaxyproject.org/singularity/meryl:1.4.1--h4ac6f70_0': + 'biocontainers/meryl:1.4.1--h4ac6f70_0' }" input: tuple val(meta), path(meryl_dbs) + val kvalue output: tuple val(meta), path("*.unionsum.meryldb"), emit: meryl_db @@ -22,6 +23,7 @@ process MERYL_UNIONSUM { def prefix = task.ext.prefix ?: "${meta.id}" """ meryl union-sum \\ + k=$kvalue \\ threads=$task.cpus \\ $args \\ output ${prefix}.unionsum.meryldb \\ @@ -32,4 +34,16 @@ process MERYL_UNIONSUM { meryl: \$( meryl --version |& sed 's/meryl //' ) END_VERSIONS """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.unionsum.meryldb + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + meryl: \$( meryl --version |& sed 's/meryl //' ) + END_VERSIONS + """ } diff --git a/modules/nf-core/meryl/unionsum/meta.yml b/modules/nf-core/meryl/unionsum/meta.yml index 9b46f7b9e51..3bb0125088d 100644 --- a/modules/nf-core/meryl/unionsum/meta.yml +++ b/modules/nf-core/meryl/unionsum/meta.yml @@ -3,13 +3,14 @@ description: A genomic k-mer counter (and sequence utility) with nice features. keywords: - k-mer - unionsum + - reference-free tools: - "meryl": description: "A genomic k-mer counter (and sequence utility) with nice features. " homepage: "https://github.com/marbl/meryl" documentation: "https://meryl.readthedocs.io/en/latest/quick-start.html" tool_dev_url: "https://github.com/marbl/meryl" - licence: "['GPL']" + licence: ["GPL"] input: - meta: type: map @@ -19,6 +20,9 @@ input: - meryl_dbs: type: directory description: Meryl k-mer databases + - kvalue: + type: integer + description: An integer value of k to use as the k-mer value. output: - meta: type: map diff --git a/modules/nf-core/meryl/unionsum/tests/main.nf.test b/modules/nf-core/meryl/unionsum/tests/main.nf.test new file mode 100644 index 00000000000..dc1bf8afa0b --- /dev/null +++ b/modules/nf-core/meryl/unionsum/tests/main.nf.test @@ -0,0 +1,123 @@ +nextflow_process { + + name "Test Process MERYL_UNIONSUM" + script "../main.nf" + process "MERYL_UNIONSUM" + + tag "modules" + tag "modules_nfcore" + tag "meryl" + tag "meryl/unionsum" + tag "meryl/count" + + test("sarscov2 - fastq - single_end") { + + setup { + run('MERYL_COUNT'){ + script "../../../../../modules/nf-core/meryl/count/main.nf" + process { + """ + input[0] = Channel.value([ + [ id: 'test', single_end: true ], // meta map + file( params.modules_testdata_base_path + "/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true ) + ]) + input[1] = Channel.value(21) + """ + } + } + } + + when { + process { + """ + input[0] = MERYL_COUNT.out.meryl_db + input[1] = Channel.value(21) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - fastq - paired_end") { + + setup { + run('MERYL_COUNT'){ + script "../../../../../modules/nf-core/meryl/count/main.nf" + process { + """ + input[0] = Channel.value([ + [ id: 'test', single_end: false ], // meta map + [ + file( params.modules_testdata_base_path + "/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true ), + file( params.modules_testdata_base_path + "/genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true ) + ] + ]) + input[1] = Channel.value(21) + """ + } + } + } + + when { + process { + """ + input[0] = MERYL_COUNT.out.meryl_db + input[1] = Channel.value(21) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - fastq- stub") { + + options "-stub" + + setup { + run('MERYL_COUNT'){ + script "../../../../../modules/nf-core/meryl/count/main.nf" + process { + """ + input[0] = Channel.value([ + [ id: 'test', single_end: true ], // meta map + file( params.modules_testdata_base_path + "/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true ) + ]) + input[1] = Channel.value(21) + """ + } + } + } + + when { + process { + """ + input[0] = MERYL_COUNT.out.meryl_db + input[1] = Channel.value(21) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/meryl/unionsum/tests/main.nf.test.snap b/modules/nf-core/meryl/unionsum/tests/main.nf.test.snap new file mode 100644 index 00000000000..522a52c97ca --- /dev/null +++ b/modules/nf-core/meryl/unionsum/tests/main.nf.test.snap @@ -0,0 +1,627 @@ +{ + "sarscov2 - fastq- stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.unionsum.meryldb:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,c97980ac5ebd37a77768c105861ad719" + ], + "meryl_db": [ + [ + { + "id": "test", + "single_end": true + }, + "test.unionsum.meryldb:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,c97980ac5ebd37a77768c105861ad719" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-27T10:19:52.291287389" + }, + "sarscov2 - fastq - single_end": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + [ + "0x000000.merylData:md5,7d95ca25a2d39a0b8fb5f71a77d7bddd", + "0x000000.merylIndex:md5,ca9b05f5b90ed432aa1134378a86f166", + "0x000001.merylData:md5,bb4e2ec7d45a2d4fa36e802b0e312965", + "0x000001.merylIndex:md5,26b3ad6909cec2061c476201a0ac04cd", + "0x000010.merylData:md5,b4b8e7a742b4634ca82d2d19928cacd6", + "0x000010.merylIndex:md5,a266e782d80833c8e685a42f07937fc7", + "0x000011.merylData:md5,bc181b55548c6d7832b65be4bed8ec56", + "0x000011.merylIndex:md5,f2bb128f3da304408c81cefb0d4de879", + "0x000100.merylData:md5,07da07cdc83420487641f7201c1593c2", + "0x000100.merylIndex:md5,f40d2c9ecf5980328cfd766b9d90019d", + "0x000101.merylData:md5,2410ff0d6604044e9175feb668e747ac", + "0x000101.merylIndex:md5,f61473e3e39e6990c30bfa53e2a63302", + "0x000110.merylData:md5,05804f66393bef8edf69143a6cd984bc", + "0x000110.merylIndex:md5,15b6e88e01e1b1abc29b54128067a938", + "0x000111.merylData:md5,a3ced1867214878de2d83dda7e805308", + "0x000111.merylIndex:md5,2998f056a5f859229229b0051cb792ec", + 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"23.10.1" + }, + "timestamp": "2024-03-27T10:19:40.09228319" + } +} \ No newline at end of file diff --git a/modules/nf-core/meryl/unionsum/tests/tags.yml b/modules/nf-core/meryl/unionsum/tests/tags.yml new file mode 100644 index 00000000000..707dd7817d7 --- /dev/null +++ b/modules/nf-core/meryl/unionsum/tests/tags.yml @@ -0,0 +1,2 @@ +meryl/unionsum: + - "modules/nf-core/meryl/unionsum/**" diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index f4ff16b7156..4805bf259cc 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -1234,9 +1234,6 @@ merquryfk/merquryfk: merquryfk/ploidyplot: - modules/nf-core/merquryfk/ploidyplot/** - tests/modules/nf-core/merquryfk/ploidyplot/** -meryl/unionsum: - - modules/nf-core/meryl/unionsum/** - - tests/modules/nf-core/meryl/unionsum/** metabat2/jgisummarizebamcontigdepths: - modules/nf-core/metabat2/jgisummarizebamcontigdepths/** - tests/modules/nf-core/metabat2/jgisummarizebamcontigdepths/** diff --git a/tests/modules/nf-core/meryl/unionsum/main.nf b/tests/modules/nf-core/meryl/unionsum/main.nf deleted file mode 100644 index e4e767375ce..00000000000 --- a/tests/modules/nf-core/meryl/unionsum/main.nf +++ /dev/null @@ -1,31 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { MERYL_COUNT } from '../../../../../modules/nf-core/meryl/count/main.nf' -include { MERYL_UNIONSUM } from '../../../../../modules/nf-core/meryl/unionsum/main.nf' - -workflow test_meryl_unionsum_single_end { - - input = [ - [ id:'test', single_end: true ], // meta map - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) - ] - - MERYL_COUNT ( input ) - MERYL_UNIONSUM ( MERYL_COUNT.out.meryl_db ) -} - -workflow test_meryl_unionsum_paired_end { - - input = [ - [ id:'test', single_end: false ], // meta map - [ - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) - ] - ] - - MERYL_COUNT ( input ) - MERYL_UNIONSUM ( MERYL_COUNT.out.meryl_db ) -} diff --git a/tests/modules/nf-core/meryl/unionsum/nextflow.config b/tests/modules/nf-core/meryl/unionsum/nextflow.config deleted file mode 100644 index 6d899c503af..00000000000 --- a/tests/modules/nf-core/meryl/unionsum/nextflow.config +++ /dev/null @@ -1,6 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - ext.args = 'k=21' - -} diff --git a/tests/modules/nf-core/meryl/unionsum/test.yml b/tests/modules/nf-core/meryl/unionsum/test.yml deleted file mode 100644 index 244b2a58644..00000000000 --- a/tests/modules/nf-core/meryl/unionsum/test.yml +++ /dev/null @@ -1,17 +0,0 @@ -- name: meryl unionsum test_meryl_unionsum_single_end - command: nextflow run ./tests/modules/nf-core/meryl/unionsum -entry test_meryl_unionsum_single_end -c ./tests/config/nextflow.config - tags: - - meryl - - meryl/unionsum - files: - - path: output/meryl/versions.yml - md5sum: 7de859c6d3a29d72f6c9c976609d0913 - -- name: meryl unionsum test_meryl_unionsum_paired_end - command: nextflow run ./tests/modules/nf-core/meryl/unionsum -entry test_meryl_unionsum_paired_end -c ./tests/config/nextflow.config - tags: - - meryl - - meryl/unionsum - files: - - path: output/meryl/versions.yml - md5sum: a16decdec014ccb9bdab69a4a1d30818