From 9e2a58d2c6a46a7d21cd5073c75d36655afba0f1 Mon Sep 17 00:00:00 2001 From: sofstam Date: Fri, 7 Feb 2025 15:27:59 +0100 Subject: [PATCH 01/11] Add sylphtax taxprof module --- .../nf-core/sylphtax/taxprof/environment.yml | 7 ++ modules/nf-core/sylphtax/taxprof/main.nf | 50 +++++++++++ modules/nf-core/sylphtax/taxprof/meta.yml | 69 +++++++++++++++ .../sylphtax/taxprof/tests/main.nf.test | 83 +++++++++++++++++++ .../sylphtax/taxprof/tests/main.nf.test.snap | 36 ++++++++ 5 files changed, 245 insertions(+) create mode 100644 modules/nf-core/sylphtax/taxprof/environment.yml create mode 100644 modules/nf-core/sylphtax/taxprof/main.nf create mode 100644 modules/nf-core/sylphtax/taxprof/meta.yml create mode 100644 modules/nf-core/sylphtax/taxprof/tests/main.nf.test create mode 100644 modules/nf-core/sylphtax/taxprof/tests/main.nf.test.snap diff --git a/modules/nf-core/sylphtax/taxprof/environment.yml b/modules/nf-core/sylphtax/taxprof/environment.yml new file mode 100644 index 00000000000..7f6ea1d2a0b --- /dev/null +++ b/modules/nf-core/sylphtax/taxprof/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - "bioconda::sylph-tax=1.1.0" diff --git a/modules/nf-core/sylphtax/taxprof/main.nf b/modules/nf-core/sylphtax/taxprof/main.nf new file mode 100644 index 00000000000..25078dcf5be --- /dev/null +++ b/modules/nf-core/sylphtax/taxprof/main.nf @@ -0,0 +1,50 @@ + +process SYLPHTAX_TAXPROF { + tag "$meta.id" + label 'process_medium' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/sylph-tax:1.1.1--pyhdfd78af_1': + 'biocontainers/sylph-tax:1.1.1--pyhdfd78af_1' }" + + input: + tuple val(meta), path(sylph_results) + path taxonomy + + output: + tuple val(meta), path("*.sylphmpa") , emit: taxprof_output + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + + """ + sylph-tax \\ + taxprof \\ + $sylph_results \\ + $args \\ + -o ${prefix}.sylphmpa \\ + -t $taxonomy + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + sylph-tax: \$(sylph-tax --version 2>&1) + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.sylphmpa + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + sylph-tax: \$(sylph-tax --version 2>&1) + END_VERSIONS + """ +} diff --git a/modules/nf-core/sylphtax/taxprof/meta.yml b/modules/nf-core/sylphtax/taxprof/meta.yml new file mode 100644 index 00000000000..fd399c99aff --- /dev/null +++ b/modules/nf-core/sylphtax/taxprof/meta.yml @@ -0,0 +1,69 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "sylphtax_taxprof" +## TODO nf-core: Add a description of the module and list keywords +description: write your description here +keywords: + - sort + - example + - genomics +tools: + - "sylphtax": + ## TODO nf-core: Add a description and other details for the software below + description: "Integrating taxonomic information into the sylph metagenome profiler." + homepage: "https://github.com/bluenote-1577/sylph-tax/blob/v1.0.0/README.md" + documentation: "https://github.com/bluenote-1577/sylph-tax/blob/v1.0.0/README.md" + tool_dev_url: "https://github.com/bluenote-1577/sylph-tax" + doi: "" + licence: ['MIT'] + identifier: + +## TODO nf-core: Add a description of all of the variables used as input +input: + # Only when we have meta + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + + ## TODO nf-core: Delete / customise this example input + - bam: + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + ontologies: + - edam: "http://edamontology.org/format_25722" + - edam: "http://edamontology.org/format_2573" + - edam: "http://edamontology.org/format_3462" + + +## TODO nf-core: Add a description of all of the variables used as output +output: + - bam: + #Only when we have meta + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + ## TODO nf-core: Delete / customise this example output + - "*.bam": + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + ontologies: + - edam: "http://edamontology.org/format_25722" + - edam: "http://edamontology.org/format_2573" + - edam: "http://edamontology.org/format_3462" + + - versions: + - "versions.yml": + type: file + description: File containing software versions + pattern: "versions.yml" + +authors: + - "@sofstam" +maintainers: + - "@sofstam" diff --git a/modules/nf-core/sylphtax/taxprof/tests/main.nf.test b/modules/nf-core/sylphtax/taxprof/tests/main.nf.test new file mode 100644 index 00000000000..c1f35438733 --- /dev/null +++ b/modules/nf-core/sylphtax/taxprof/tests/main.nf.test @@ -0,0 +1,83 @@ +nextflow_process { + + name "Test Process SYLPHTAX_TAXPROF" + script "../main.nf" + process "SYLPHTAX_TAXPROF" + + tag "modules" + tag "modules_nfcore" + tag "sylphtax" + tag "sylphtax/taxprof" + + + test("sarscov2 illumina single-end [fastq_gz]") { + setup { + run("SYLPH_PROFILE") { + script "../../../sylph/profile/main.nf" + process { + """ + input[0] = [ [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] + ] + input[1] = file(params.modules_testdata_base_path +'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + """ + } + } + } + when { + process { + """ + input[0] = SYLPH_PROFILE.out.profile_out + input[1] = file('https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/sylph/test_taxonomy.tsv.gz', checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.taxprof_output).match() } + ) + } + + } + + test("stub sarscov2 illumina single-end [fastq_gz]") { + + options '-stub' + + setup { + run("SYLPH_PROFILE") { + script "../../../sylph/profile/main.nf" + process { + """ + input[0] = [ [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] + ] + input[1] = file(params.modules_testdata_base_path +'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + """ + } + } + } + when { + process { + """ + input[0] = SYLPH_PROFILE.out.profile_out + input[1] = file('https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/sylph/test_taxonomy.tsv.gz', checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.taxprof_output).match() } + ) + } + } + +} diff --git a/modules/nf-core/sylphtax/taxprof/tests/main.nf.test.snap b/modules/nf-core/sylphtax/taxprof/tests/main.nf.test.snap new file mode 100644 index 00000000000..6ef76293389 --- /dev/null +++ b/modules/nf-core/sylphtax/taxprof/tests/main.nf.test.snap @@ -0,0 +1,36 @@ +{ + "stub sarscov2 illumina single-end [fastq_gz]": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.sylphmpa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-02-07T15:20:28.349616782" + }, + "sarscov2 illumina single-end [fastq_gz]": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.sylphmpatest_1.fastq.gz.sylphmpa:md5,797e3463eeb9a2e8f91de9b842cd421d" + ] + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-02-07T15:20:20.639766288" + } +} \ No newline at end of file From ceb7dbee40c4de435d2ae7bfdb567f41d377b7d5 Mon Sep 17 00:00:00 2001 From: sofstam Date: Fri, 7 Feb 2025 16:09:15 +0100 Subject: [PATCH 02/11] Fix linting --- modules/nf-core/sylphtax/taxprof/meta.yml | 109 ++++++++---------- .../sylphtax/taxprof/tests/main.nf.test | 12 +- .../sylphtax/taxprof/tests/main.nf.test.snap | 10 +- 3 files changed, 64 insertions(+), 67 deletions(-) diff --git a/modules/nf-core/sylphtax/taxprof/meta.yml b/modules/nf-core/sylphtax/taxprof/meta.yml index fd399c99aff..ce9be822831 100644 --- a/modules/nf-core/sylphtax/taxprof/meta.yml +++ b/modules/nf-core/sylphtax/taxprof/meta.yml @@ -1,69 +1,52 @@ ---- -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json -name: "sylphtax_taxprof" -## TODO nf-core: Add a description of the module and list keywords -description: write your description here +name: sylphtax_taxprof +description: Incorporates taxonomy into sylph metagenomic classifier keywords: - - sort - - example - - genomics +- taxonomy +- sylph +- metagenomics tools: - - "sylphtax": - ## TODO nf-core: Add a description and other details for the software below - description: "Integrating taxonomic information into the sylph metagenome profiler." - homepage: "https://github.com/bluenote-1577/sylph-tax/blob/v1.0.0/README.md" - documentation: "https://github.com/bluenote-1577/sylph-tax/blob/v1.0.0/README.md" - tool_dev_url: "https://github.com/bluenote-1577/sylph-tax" - doi: "" - licence: ['MIT'] - identifier: - -## TODO nf-core: Add a description of all of the variables used as input +- sylphtax: + description: Integrating taxonomic information into the sylph metagenome profiler. + homepage: https://github.com/bluenote-1577/sylph-tax?tab=readme-ov-file + documentation: https://sylph-docs.github.io/sylph-tax/ + licence: ["MIT"] + identifier: '' input: - # Only when we have meta - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - ## TODO nf-core: Delete / customise this example input - - bam: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - ontologies: - - edam: "http://edamontology.org/format_25722" - - edam: "http://edamontology.org/format_2573" - - edam: "http://edamontology.org/format_3462" - - -## TODO nf-core: Add a description of all of the variables used as output +- - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - sylph_results: + type: file + description: Output results from sylph classifier. The databases used for sylph + must be the same as the -t option. + pattern: "*.{tsv}" +- - taxonomy: + type: file + description: A list of sylph-tax identifiers (e.g. GTDB_r220 or IMGVR_4.1). + Multiple taxonomy metadata files can be input. Custom taxonomy files are also + possible. output: - - bam: - #Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - ## TODO nf-core: Delete / customise this example output - - "*.bam": - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - ontologies: - - edam: "http://edamontology.org/format_25722" - - edam: "http://edamontology.org/format_2573" - - edam: "http://edamontology.org/format_3462" - - - versions: - - "versions.yml": - type: file - description: File containing software versions - pattern: "versions.yml" - +- taxprof_output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*{.sylphmpa}" + - '*.sylphmpa': + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*{.sylphmpa}" +- versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@sofstam" +- "@sofstam" maintainers: - - "@sofstam" +- "@sofstam" diff --git a/modules/nf-core/sylphtax/taxprof/tests/main.nf.test b/modules/nf-core/sylphtax/taxprof/tests/main.nf.test index c1f35438733..e0d4805251a 100644 --- a/modules/nf-core/sylphtax/taxprof/tests/main.nf.test +++ b/modules/nf-core/sylphtax/taxprof/tests/main.nf.test @@ -6,6 +6,8 @@ nextflow_process { tag "modules" tag "modules_nfcore" + tag "sylph" + tag "sylph/profile" tag "sylphtax" tag "sylphtax/taxprof" @@ -38,7 +40,10 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.taxprof_output).match() } + { assert snapshot( + process.out.versions, + process.out.taxprof_output + ).match() } ) } @@ -75,7 +80,10 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.taxprof_output).match() } + { assert snapshot( + process.out.versions, + process.out.taxprof_output + ).match() } ) } } diff --git a/modules/nf-core/sylphtax/taxprof/tests/main.nf.test.snap b/modules/nf-core/sylphtax/taxprof/tests/main.nf.test.snap index 6ef76293389..d3c9ef90156 100644 --- a/modules/nf-core/sylphtax/taxprof/tests/main.nf.test.snap +++ b/modules/nf-core/sylphtax/taxprof/tests/main.nf.test.snap @@ -1,6 +1,9 @@ { "stub sarscov2 illumina single-end [fastq_gz]": { "content": [ + [ + "versions.yml:md5,c24c1e619994c7d721ef2c1048783565" + ], [ [ { @@ -14,10 +17,13 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-07T15:20:28.349616782" + "timestamp": "2025-02-07T16:06:15.822788243" }, "sarscov2 illumina single-end [fastq_gz]": { "content": [ + [ + "versions.yml:md5,c24c1e619994c7d721ef2c1048783565" + ], [ [ { @@ -31,6 +37,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-07T15:20:20.639766288" + "timestamp": "2025-02-07T16:06:07.453121154" } } \ No newline at end of file From f89a0e9b93d65cb20cff294b825f866ef01b24e1 Mon Sep 17 00:00:00 2001 From: sofstam Date: Fri, 7 Feb 2025 16:15:50 +0100 Subject: [PATCH 03/11] Update snapshot --- modules/nf-core/sylphtax/taxprof/tests/main.nf.test.snap | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/sylphtax/taxprof/tests/main.nf.test.snap b/modules/nf-core/sylphtax/taxprof/tests/main.nf.test.snap index d3c9ef90156..7a0564c5f18 100644 --- a/modules/nf-core/sylphtax/taxprof/tests/main.nf.test.snap +++ b/modules/nf-core/sylphtax/taxprof/tests/main.nf.test.snap @@ -17,7 +17,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-07T16:06:15.822788243" + "timestamp": "2025-02-07T16:15:14.340158328" }, "sarscov2 illumina single-end [fastq_gz]": { "content": [ @@ -37,6 +37,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-07T16:06:07.453121154" + "timestamp": "2025-02-07T16:15:06.149734399" } } \ No newline at end of file From 9a8fd52a98e9fe2d2d2759b60995cb60b7f24299 Mon Sep 17 00:00:00 2001 From: sofstam Date: Fri, 7 Feb 2025 16:34:59 +0100 Subject: [PATCH 04/11] Update snapshot --- modules/nf-core/sylphtax/taxprof/tests/main.nf.test.snap | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/sylphtax/taxprof/tests/main.nf.test.snap b/modules/nf-core/sylphtax/taxprof/tests/main.nf.test.snap index 7a0564c5f18..6dc76847c2c 100644 --- a/modules/nf-core/sylphtax/taxprof/tests/main.nf.test.snap +++ b/modules/nf-core/sylphtax/taxprof/tests/main.nf.test.snap @@ -39,4 +39,4 @@ }, "timestamp": "2025-02-07T16:15:06.149734399" } -} \ No newline at end of file +} From 4bc140a030e2fac7001a943f1f2dacd8ed124603 Mon Sep 17 00:00:00 2001 From: sofstam Date: Thu, 13 Feb 2025 10:10:02 +0100 Subject: [PATCH 05/11] Update versions --- modules/nf-core/sylphtax/taxprof/main.nf | 2 +- modules/nf-core/sylphtax/taxprof/tests/main.nf.test.snap | 8 ++++---- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/modules/nf-core/sylphtax/taxprof/main.nf b/modules/nf-core/sylphtax/taxprof/main.nf index 25078dcf5be..34abc815a2f 100644 --- a/modules/nf-core/sylphtax/taxprof/main.nf +++ b/modules/nf-core/sylphtax/taxprof/main.nf @@ -33,7 +33,7 @@ process SYLPHTAX_TAXPROF { cat <<-END_VERSIONS > versions.yml "${task.process}": - sylph-tax: \$(sylph-tax --version 2>&1) + sylph-tax: \$(sylph-tax --version 2>&1 | sed -n 's/.*sylph-tax: \\([0-9]\\+\\.[0-9]\\+\\.[0-9]\\+\\).*/\\1/p') END_VERSIONS """ diff --git a/modules/nf-core/sylphtax/taxprof/tests/main.nf.test.snap b/modules/nf-core/sylphtax/taxprof/tests/main.nf.test.snap index 6dc76847c2c..7687834630e 100644 --- a/modules/nf-core/sylphtax/taxprof/tests/main.nf.test.snap +++ b/modules/nf-core/sylphtax/taxprof/tests/main.nf.test.snap @@ -17,12 +17,12 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-07T16:15:14.340158328" + "timestamp": "2025-02-13T10:02:39.502519432" }, "sarscov2 illumina single-end [fastq_gz]": { "content": [ [ - "versions.yml:md5,c24c1e619994c7d721ef2c1048783565" + "versions.yml:md5,172678e29479ce135dfc6b7180dfb919" ], [ [ @@ -37,6 +37,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-07T16:15:06.149734399" + "timestamp": "2025-02-13T10:02:31.088892244" } -} +} \ No newline at end of file From 61f1ec44cb92f614c6fba6d0ea458c56e6e13366 Mon Sep 17 00:00:00 2001 From: sofstam Date: Thu, 13 Feb 2025 10:50:17 +0100 Subject: [PATCH 06/11] Correct sylphtax version --- modules/nf-core/sylphtax/taxprof/main.nf | 4 ++-- modules/nf-core/sylphtax/taxprof/tests/main.nf.test.snap | 8 ++++---- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/modules/nf-core/sylphtax/taxprof/main.nf b/modules/nf-core/sylphtax/taxprof/main.nf index 34abc815a2f..fabbdd29473 100644 --- a/modules/nf-core/sylphtax/taxprof/main.nf +++ b/modules/nf-core/sylphtax/taxprof/main.nf @@ -33,7 +33,7 @@ process SYLPHTAX_TAXPROF { cat <<-END_VERSIONS > versions.yml "${task.process}": - sylph-tax: \$(sylph-tax --version 2>&1 | sed -n 's/.*sylph-tax: \\([0-9]\\+\\.[0-9]\\+\\.[0-9]\\+\\).*/\\1/p') + sylph-tax: \$(sylph-tax --version 2>&1 | sed -n 's/.*\\([0-9]\\+\\.[0-9]\\+\\.[0-9]\\+\\).*/\\1/p' | head -n 1) END_VERSIONS """ @@ -44,7 +44,7 @@ process SYLPHTAX_TAXPROF { cat <<-END_VERSIONS > versions.yml "${task.process}": - sylph-tax: \$(sylph-tax --version 2>&1) + sylph-tax: \$(sylph-tax --version 2>&1 | sed -n 's/.*\\([0-9]\\+\\.[0-9]\\+\\.[0-9]\\+\\).*/\\1/p' | head -n 1) END_VERSIONS """ } diff --git a/modules/nf-core/sylphtax/taxprof/tests/main.nf.test.snap b/modules/nf-core/sylphtax/taxprof/tests/main.nf.test.snap index 7687834630e..7b4b88ecf81 100644 --- a/modules/nf-core/sylphtax/taxprof/tests/main.nf.test.snap +++ b/modules/nf-core/sylphtax/taxprof/tests/main.nf.test.snap @@ -2,7 +2,7 @@ "stub sarscov2 illumina single-end [fastq_gz]": { "content": [ [ - "versions.yml:md5,c24c1e619994c7d721ef2c1048783565" + "versions.yml:md5,3400e2e5e4eaa5502c6984e78e718168" ], [ [ @@ -17,12 +17,12 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-13T10:02:39.502519432" + "timestamp": "2025-02-13T10:48:42.404745261" }, "sarscov2 illumina single-end [fastq_gz]": { "content": [ [ - "versions.yml:md5,172678e29479ce135dfc6b7180dfb919" + "versions.yml:md5,3400e2e5e4eaa5502c6984e78e718168" ], [ [ @@ -37,6 +37,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-13T10:02:31.088892244" + "timestamp": "2025-02-13T10:48:34.701505179" } } \ No newline at end of file From c30eccfe8a8823ae3c76596e4f7fbe9843b81886 Mon Sep 17 00:00:00 2001 From: sofstam Date: Thu, 13 Feb 2025 11:51:06 +0100 Subject: [PATCH 07/11] Update versions --- modules/nf-core/sylphtax/taxprof/tests/main.nf.test | 4 ++-- .../nf-core/sylphtax/taxprof/tests/main.nf.test.snap | 12 ++++-------- 2 files changed, 6 insertions(+), 10 deletions(-) diff --git a/modules/nf-core/sylphtax/taxprof/tests/main.nf.test b/modules/nf-core/sylphtax/taxprof/tests/main.nf.test index e0d4805251a..08930a2b6aa 100644 --- a/modules/nf-core/sylphtax/taxprof/tests/main.nf.test +++ b/modules/nf-core/sylphtax/taxprof/tests/main.nf.test @@ -41,7 +41,7 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - process.out.versions, + path(process.out.versions[0]).text.contains("1.1.1"), process.out.taxprof_output ).match() } ) @@ -81,7 +81,7 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - process.out.versions, + path(process.out.versions[0]).text.contains("1.1.1"), process.out.taxprof_output ).match() } ) diff --git a/modules/nf-core/sylphtax/taxprof/tests/main.nf.test.snap b/modules/nf-core/sylphtax/taxprof/tests/main.nf.test.snap index 7b4b88ecf81..88ad778c2eb 100644 --- a/modules/nf-core/sylphtax/taxprof/tests/main.nf.test.snap +++ b/modules/nf-core/sylphtax/taxprof/tests/main.nf.test.snap @@ -1,9 +1,7 @@ { "stub sarscov2 illumina single-end [fastq_gz]": { "content": [ - [ - "versions.yml:md5,3400e2e5e4eaa5502c6984e78e718168" - ], + false, [ [ { @@ -17,13 +15,11 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-13T10:48:42.404745261" + "timestamp": "2025-02-13T11:50:11.302386741" }, "sarscov2 illumina single-end [fastq_gz]": { "content": [ - [ - "versions.yml:md5,3400e2e5e4eaa5502c6984e78e718168" - ], + false, [ [ { @@ -37,6 +33,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-13T10:48:34.701505179" + "timestamp": "2025-02-13T11:44:29.769225699" } } \ No newline at end of file From 67945cd7fc0952f23c1e9ddabfa27c5d0ea1ed9b Mon Sep 17 00:00:00 2001 From: sofstam Date: Thu, 13 Feb 2025 12:49:00 +0100 Subject: [PATCH 08/11] Update snapshot --- modules/nf-core/sylphtax/taxprof/tests/main.nf.test.snap | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/sylphtax/taxprof/tests/main.nf.test.snap b/modules/nf-core/sylphtax/taxprof/tests/main.nf.test.snap index 88ad778c2eb..75f7195c647 100644 --- a/modules/nf-core/sylphtax/taxprof/tests/main.nf.test.snap +++ b/modules/nf-core/sylphtax/taxprof/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-13T11:50:11.302386741" + "timestamp": "2025-02-13T12:06:51.477077936" }, "sarscov2 illumina single-end [fastq_gz]": { "content": [ @@ -33,6 +33,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-13T11:44:29.769225699" + "timestamp": "2025-02-13T12:02:42.711352257" } } \ No newline at end of file From cb0827e2ca91ef340f5451963374e6c1e7b4a7a6 Mon Sep 17 00:00:00 2001 From: sofstam Date: Thu, 13 Feb 2025 13:30:40 +0100 Subject: [PATCH 09/11] Update snapshots --- modules/nf-core/sylphtax/taxprof/environment.yml | 2 +- modules/nf-core/sylphtax/taxprof/main.nf | 4 ++-- modules/nf-core/sylphtax/taxprof/tests/main.nf.test | 4 ++-- .../nf-core/sylphtax/taxprof/tests/main.nf.test.snap | 12 ++++++++---- 4 files changed, 13 insertions(+), 9 deletions(-) diff --git a/modules/nf-core/sylphtax/taxprof/environment.yml b/modules/nf-core/sylphtax/taxprof/environment.yml index 7f6ea1d2a0b..f35891d9ae0 100644 --- a/modules/nf-core/sylphtax/taxprof/environment.yml +++ b/modules/nf-core/sylphtax/taxprof/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::sylph-tax=1.1.0" + - "bioconda::sylph-tax=1.1.2" diff --git a/modules/nf-core/sylphtax/taxprof/main.nf b/modules/nf-core/sylphtax/taxprof/main.nf index fabbdd29473..90a116a7eea 100644 --- a/modules/nf-core/sylphtax/taxprof/main.nf +++ b/modules/nf-core/sylphtax/taxprof/main.nf @@ -5,8 +5,8 @@ process SYLPHTAX_TAXPROF { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/sylph-tax:1.1.1--pyhdfd78af_1': - 'biocontainers/sylph-tax:1.1.1--pyhdfd78af_1' }" + 'https://depot.galaxyproject.org/singularity/sylph-tax:1.1.2--pyhdfd78af_0': + 'biocontainers/sylph-tax:1.1.2--pyhdfd78af_0' }" input: tuple val(meta), path(sylph_results) diff --git a/modules/nf-core/sylphtax/taxprof/tests/main.nf.test b/modules/nf-core/sylphtax/taxprof/tests/main.nf.test index 08930a2b6aa..e0d4805251a 100644 --- a/modules/nf-core/sylphtax/taxprof/tests/main.nf.test +++ b/modules/nf-core/sylphtax/taxprof/tests/main.nf.test @@ -41,7 +41,7 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - path(process.out.versions[0]).text.contains("1.1.1"), + process.out.versions, process.out.taxprof_output ).match() } ) @@ -81,7 +81,7 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - path(process.out.versions[0]).text.contains("1.1.1"), + process.out.versions, process.out.taxprof_output ).match() } ) diff --git a/modules/nf-core/sylphtax/taxprof/tests/main.nf.test.snap b/modules/nf-core/sylphtax/taxprof/tests/main.nf.test.snap index 75f7195c647..d5db49e44dd 100644 --- a/modules/nf-core/sylphtax/taxprof/tests/main.nf.test.snap +++ b/modules/nf-core/sylphtax/taxprof/tests/main.nf.test.snap @@ -1,7 +1,9 @@ { "stub sarscov2 illumina single-end [fastq_gz]": { "content": [ - false, + [ + "versions.yml:md5,976fae8d146f4f3087e2a090703f09b9" + ], [ [ { @@ -15,11 +17,13 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-13T12:06:51.477077936" + "timestamp": "2025-02-13T13:27:49.708058346" }, "sarscov2 illumina single-end [fastq_gz]": { "content": [ - false, + [ + "versions.yml:md5,976fae8d146f4f3087e2a090703f09b9" + ], [ [ { @@ -33,6 +37,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-13T12:02:42.711352257" + "timestamp": "2025-02-13T13:22:19.31463228" } } \ No newline at end of file From 73021aac1ddf9547e35ac7b80f52506daab3fc1f Mon Sep 17 00:00:00 2001 From: Sofia Stamouli <91951607+sofstam@users.noreply.github.com> Date: Thu, 13 Feb 2025 14:23:02 +0100 Subject: [PATCH 10/11] Update modules/nf-core/sylphtax/taxprof/main.nf Co-authored-by: Jasmin Frangenberg <73216762+jasmezz@users.noreply.github.com> --- modules/nf-core/sylphtax/taxprof/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/sylphtax/taxprof/main.nf b/modules/nf-core/sylphtax/taxprof/main.nf index 90a116a7eea..95f197bafae 100644 --- a/modules/nf-core/sylphtax/taxprof/main.nf +++ b/modules/nf-core/sylphtax/taxprof/main.nf @@ -13,8 +13,8 @@ process SYLPHTAX_TAXPROF { path taxonomy output: - tuple val(meta), path("*.sylphmpa") , emit: taxprof_output - path "versions.yml" , emit: versions + tuple val(meta), path("*.sylphmpa"), emit: taxprof_output + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when From 160d410da01ea8317e3f1429e264715322f7a05d Mon Sep 17 00:00:00 2001 From: Sofia Stamouli <91951607+sofstam@users.noreply.github.com> Date: Thu, 13 Feb 2025 14:24:05 +0100 Subject: [PATCH 11/11] Update modules/nf-core/sylphtax/taxprof/meta.yml Co-authored-by: Jasmin Frangenberg <73216762+jasmezz@users.noreply.github.com> --- modules/nf-core/sylphtax/taxprof/meta.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/modules/nf-core/sylphtax/taxprof/meta.yml b/modules/nf-core/sylphtax/taxprof/meta.yml index ce9be822831..e4ee39ba0db 100644 --- a/modules/nf-core/sylphtax/taxprof/meta.yml +++ b/modules/nf-core/sylphtax/taxprof/meta.yml @@ -19,8 +19,7 @@ input: e.g. `[ id:'sample1', single_end:false ]` - sylph_results: type: file - description: Output results from sylph classifier. The databases used for sylph - must be the same as the -t option. + description: Output results from sylph classifier. The database file(s) used to create this file with sylph must be the same as those of the taxonomy input channel of this module. pattern: "*.{tsv}" - - taxonomy: type: file