From 15d27bd0ba59330c3b024a8432b84672d475517d Mon Sep 17 00:00:00 2001 From: SkyLexS Date: Wed, 4 Mar 2026 00:37:44 +0200 Subject: [PATCH 01/12] Updating bigslice --- modules/nf-core/bigslice/main.nf | 17 +++++++--- modules/nf-core/bigslice/tests/main.nf.test | 20 +++++++++--- .../nf-core/bigslice/tests/main.nf.test.snap | 31 +++---------------- 3 files changed, 32 insertions(+), 36 deletions(-) diff --git a/modules/nf-core/bigslice/main.nf b/modules/nf-core/bigslice/main.nf index a1782087d0bb..73ede780ffed 100644 --- a/modules/nf-core/bigslice/main.nf +++ b/modules/nf-core/bigslice/main.nf @@ -9,13 +9,13 @@ process BIGSLICE { 'biocontainers/bigslice:2.0.2--pyh8ed023e_0' }" input: - tuple val(meta), path(bgc) + tuple val(meta), path(bgc, stageAs: 'bgc_files/*') path(hmmdb) output: tuple val(meta), path("${prefix}/result/data.db") , emit: db tuple val(meta), path("${prefix}/result/tmp/**/*.fa"), emit: fa - tuple val("${task.process}"), val('bigslice'), eval("echo 2.0.2"), topic: versions, emit: versions_bigslice + tuple val("${task.process}"), val('bigslice'), eval("echo 2.0.2"), topic: versions when: task.ext.when == null || task.ext.when @@ -23,11 +23,20 @@ process BIGSLICE { script: def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}" + def sample = meta.id """ + mkdir -p input/dataset/${sample} input/taxonomy + cp bgc_files/* input/dataset/${sample}/ + + printf "# dataset_name\\tdataset_path\\ttaxonomy_path\\tdescription\\n" > input/datasets.tsv + printf "dataset\\tdataset\\ttaxonomy/taxonomy.tsv\\tBGC dataset\\n" >> input/datasets.tsv + + touch input/taxonomy/taxonomy.tsv + bigslice \\ $args \\ --num_threads ${task.cpus} \\ - -i ${bgc} \\ + -i input \\ --program_db_folder ${hmmdb} \\ ${prefix} """ @@ -42,4 +51,4 @@ process BIGSLICE { touch ${prefix}/result/data.db touch ${prefix}/result/tmp/2e555308dfc411186cf012334262f127/test.fa """ -} +} \ No newline at end of file diff --git a/modules/nf-core/bigslice/tests/main.nf.test b/modules/nf-core/bigslice/tests/main.nf.test index 354301c85ba6..e137e99bc7f7 100644 --- a/modules/nf-core/bigslice/tests/main.nf.test +++ b/modules/nf-core/bigslice/tests/main.nf.test @@ -60,7 +60,12 @@ nextflow_process { when { process { """ - input[0] = UNTAR_GBK.out.untar + // Flatten the GBK directory into a list of individual GBK files with meta + input[0] = UNTAR_GBK.out.untar.map { meta, dir -> + def gbk_files = [] + dir.eachFileRecurse { if (it.name.endsWith('.gbk')) gbk_files << it } + [ meta, gbk_files ] + } input[1] = UNTAR_HMMDB.out.untar.map{ it -> it[1] } """ } @@ -72,7 +77,7 @@ nextflow_process { { assert snapshot( file(process.out.db[0][1]).name, process.out.fa[0][1].size(), - process.out.findAll { key, val -> key.startsWith("versions")} + process.out.versions ).match() } ) } @@ -86,7 +91,12 @@ nextflow_process { when { process { """ - input[0] = UNTAR_GBK.out.untar + // Flatten the GBK directory into a list of individual GBK files with meta + input[0] = UNTAR_GBK.out.untar.map { meta, dir -> + def gbk_files = [] + dir.eachFileRecurse { if (it.name.endsWith('.gbk')) gbk_files << it } + [ meta, gbk_files ] + } input[1] = UNTAR_HMMDB.out.untar.map{ it -> it[1] } """ } @@ -97,11 +107,11 @@ nextflow_process { assertAll( { assert snapshot( process.out, - process.out.findAll { key, val -> key.startsWith("versions")} + process.out.versions ).match() } ) } } -} +} \ No newline at end of file diff --git a/modules/nf-core/bigslice/tests/main.nf.test.snap b/modules/nf-core/bigslice/tests/main.nf.test.snap index cc26a10338d3..d6e9f2b78cad 100644 --- a/modules/nf-core/bigslice/tests/main.nf.test.snap +++ b/modules/nf-core/bigslice/tests/main.nf.test.snap @@ -40,49 +40,26 @@ }, "test.fa:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ], - "versions_bigslice": [ - [ - "BIGSLICE", - "bigslice", - "2.0.2" - ] ] }, - { - "versions_bigslice": [ - [ - "BIGSLICE", - "bigslice", - "2.0.2" - ] - ] - } + null ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-02-06T15:13:53.99145463" + "timestamp": "2026-03-04T00:23:22.776974908" }, "streptomyces_coelicolor - bigslice - gbk": { "content": [ "data.db", 40, - { - "versions_bigslice": [ - [ - "BIGSLICE", - "bigslice", - "2.0.2" - ] - ] - } + null ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-02-06T15:26:29.769543832" + "timestamp": "2026-03-04T00:23:10.410022744" } } \ No newline at end of file From 4edc137ffee2a18475e3245835007e64d08ec102 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 4 Mar 2026 06:58:55 +0000 Subject: [PATCH 02/12] [automated] Fix linting with Prettier --- modules/nf-core/bigslice/main.nf | 2 +- modules/nf-core/bigslice/tests/main.nf.test | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/bigslice/main.nf b/modules/nf-core/bigslice/main.nf index 73ede780ffed..232c7d226c6d 100644 --- a/modules/nf-core/bigslice/main.nf +++ b/modules/nf-core/bigslice/main.nf @@ -51,4 +51,4 @@ process BIGSLICE { touch ${prefix}/result/data.db touch ${prefix}/result/tmp/2e555308dfc411186cf012334262f127/test.fa """ -} \ No newline at end of file +} diff --git a/modules/nf-core/bigslice/tests/main.nf.test b/modules/nf-core/bigslice/tests/main.nf.test index e137e99bc7f7..ebb258beb8df 100644 --- a/modules/nf-core/bigslice/tests/main.nf.test +++ b/modules/nf-core/bigslice/tests/main.nf.test @@ -114,4 +114,4 @@ nextflow_process { } -} \ No newline at end of file +} From 2d142cfadc82bd4ba614595b0b4a8b7a07e7550a Mon Sep 17 00:00:00 2001 From: SkyLexS Date: Wed, 4 Mar 2026 09:50:20 +0200 Subject: [PATCH 03/12] Linting and modifing the bigslice version emiting --- modules/nf-core/bigslice/main.nf | 2 +- modules/nf-core/bigslice/tests/main.nf.test | 4 +-- .../nf-core/bigslice/tests/main.nf.test.snap | 31 ++++++++++++++++--- 3 files changed, 30 insertions(+), 7 deletions(-) diff --git a/modules/nf-core/bigslice/main.nf b/modules/nf-core/bigslice/main.nf index 232c7d226c6d..dc88bcc51142 100644 --- a/modules/nf-core/bigslice/main.nf +++ b/modules/nf-core/bigslice/main.nf @@ -15,7 +15,7 @@ process BIGSLICE { output: tuple val(meta), path("${prefix}/result/data.db") , emit: db tuple val(meta), path("${prefix}/result/tmp/**/*.fa"), emit: fa - tuple val("${task.process}"), val('bigslice'), eval("echo 2.0.2"), topic: versions + tuple val("${task.process}"), val('bigslice'), eval("echo 2.0.2"), topic: versions, emit: versions_bigslice when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/bigslice/tests/main.nf.test b/modules/nf-core/bigslice/tests/main.nf.test index ebb258beb8df..19bcb011abe5 100644 --- a/modules/nf-core/bigslice/tests/main.nf.test +++ b/modules/nf-core/bigslice/tests/main.nf.test @@ -77,7 +77,7 @@ nextflow_process { { assert snapshot( file(process.out.db[0][1]).name, process.out.fa[0][1].size(), - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions")} ).match() } ) } @@ -107,7 +107,7 @@ nextflow_process { assertAll( { assert snapshot( process.out, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions")} ).match() } ) } diff --git a/modules/nf-core/bigslice/tests/main.nf.test.snap b/modules/nf-core/bigslice/tests/main.nf.test.snap index d6e9f2b78cad..c678d7f89ce5 100644 --- a/modules/nf-core/bigslice/tests/main.nf.test.snap +++ b/modules/nf-core/bigslice/tests/main.nf.test.snap @@ -40,26 +40,49 @@ }, "test.fa:md5,d41d8cd98f00b204e9800998ecf8427e" ] + ], + "versions_bigslice": [ + [ + "BIGSLICE", + "bigslice", + "2.0.2" + ] ] }, - null + { + "versions_bigslice": [ + [ + "BIGSLICE", + "bigslice", + "2.0.2" + ] + ] + } ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-03-04T00:23:22.776974908" + "timestamp": "2026-03-04T09:47:43.387153103" }, "streptomyces_coelicolor - bigslice - gbk": { "content": [ "data.db", 40, - null + { + "versions_bigslice": [ + [ + "BIGSLICE", + "bigslice", + "2.0.2" + ] + ] + } ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-03-04T00:23:10.410022744" + "timestamp": "2026-03-04T09:47:30.918713387" } } \ No newline at end of file From 4e0e985c117874933021f058bf473c74c610043a Mon Sep 17 00:00:00 2001 From: SkyLexS Date: Tue, 24 Mar 2026 13:59:18 +0200 Subject: [PATCH 04/12] Updated the bigslice module --- modules/nf-core/bigslice/main.nf | 26 +++++++++++++++---- modules/nf-core/bigslice/meta.yml | 22 +++++++++++----- modules/nf-core/bigslice/tests/main.nf.test | 1 + .../nf-core/bigslice/tests/main.nf.test.snap | 23 +++++++++++++++- 4 files changed, 60 insertions(+), 12 deletions(-) diff --git a/modules/nf-core/bigslice/main.nf b/modules/nf-core/bigslice/main.nf index dc88bcc51142..6aec267bce8f 100644 --- a/modules/nf-core/bigslice/main.nf +++ b/modules/nf-core/bigslice/main.nf @@ -13,17 +13,25 @@ process BIGSLICE { path(hmmdb) output: - tuple val(meta), path("${prefix}/result/data.db") , emit: db + tuple val(meta), path("${prefix}/result/data.db") , emit: db tuple val(meta), path("${prefix}/result/tmp/**/*.fa"), emit: fa + tuple val(meta), path("${prefix}/result/tsv_export") , emit: tsv tuple val("${task.process}"), val('bigslice'), eval("echo 2.0.2"), topic: versions, emit: versions_bigslice when: task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' - prefix = task.ext.prefix ?: "${meta.id}" + def args = task.ext.args ?: '' + def args2 = task.ext.args2 ?: '' + prefix = task.ext.prefix ?: "${meta.id}" def sample = meta.id + def export_tsv_cmd = args2 ? """ + bigslice \\ + --export-tsv ${prefix}/result/tsv_export \\ + --program_db_folder ${hmmdb} \\ + ${prefix} + """ : '' """ mkdir -p input/dataset/${sample} input/taxonomy cp bgc_files/* input/dataset/${sample}/ @@ -39,16 +47,24 @@ process BIGSLICE { -i input \\ --program_db_folder ${hmmdb} \\ ${prefix} + + mkdir -p ${prefix}/result/tsv_export + ${export_tsv_cmd} """ stub: - def args = task.ext.args ?: '' - prefix = task.ext.prefix ?: "${meta.id}" + def args = task.ext.args ?: '' + def args2 = task.ext.args2 ?: '' + prefix = task.ext.prefix ?: "${meta.id}" """ echo $args mkdir -p ${prefix}/result/tmp/2e555308dfc411186cf012334262f127 + mkdir -p ${prefix}/result/tsv_export touch ${prefix}/result/data.db touch ${prefix}/result/tmp/2e555308dfc411186cf012334262f127/test.fa + if [ -n "${args2}" ]; then + touch ${prefix}/result/tsv_export/bgcs.tsv + fi """ } diff --git a/modules/nf-core/bigslice/meta.yml b/modules/nf-core/bigslice/meta.yml index 518f4bf38313..9af5043b0775 100644 --- a/modules/nf-core/bigslice/meta.yml +++ b/modules/nf-core/bigslice/meta.yml @@ -24,13 +24,12 @@ input: Groovy Map containing sample information e.g. `[ id:'sample1' ]` - bgc: - type: directory + type: file description: | - Path to a folder containing genomic regions in GenBank format, structured for BiG-SLiCE. - Each genome should have its own subfolder with region `.gbk` files. - The folder should also contain a datasets.tsv, and a taxonomy folder, with TSV taxonomy files per dataset. - See the tool's wiki for more information: https://github.com/medema-group/bigslice/wiki/Input-folder - pattern: "*" + List of GenBank (.gbk) files containing genomic region annotations for BiG-SLiCE input. + Each file represents a BGC region. The module internally organises them into the required + BiG-SLiCE input folder structure (datasets.tsv and taxonomy TSV). + pattern: "*.gbk" - hmmdb: type: directory description: | @@ -61,6 +60,17 @@ output: pattern: "*.fa" ontologies: - edam: "http://edamontology.org/format_1929" # FASTA + tsv: + - - meta: + type: map + description: Groovy Map containing sample/dataset information + - ${prefix}/result/tsv_export: + type: directory + description: | + Directory containing TSV exports of all parsed BGC metadata, vectorized + features and clustering results. The directory is always created; files + are only present when `--export-tsv` is passed via `task.ext.args2`. + pattern: "tsv_export" versions_bigslice: - - ${task.process}: type: string diff --git a/modules/nf-core/bigslice/tests/main.nf.test b/modules/nf-core/bigslice/tests/main.nf.test index 19bcb011abe5..08362ece6ee4 100644 --- a/modules/nf-core/bigslice/tests/main.nf.test +++ b/modules/nf-core/bigslice/tests/main.nf.test @@ -77,6 +77,7 @@ nextflow_process { { assert snapshot( file(process.out.db[0][1]).name, process.out.fa[0][1].size(), + file(process.out.tsv[0][1]).isDirectory(), process.out.findAll { key, val -> key.startsWith("versions")} ).match() } ) diff --git a/modules/nf-core/bigslice/tests/main.nf.test.snap b/modules/nf-core/bigslice/tests/main.nf.test.snap index c678d7f89ce5..bb02cb917332 100644 --- a/modules/nf-core/bigslice/tests/main.nf.test.snap +++ b/modules/nf-core/bigslice/tests/main.nf.test.snap @@ -19,6 +19,16 @@ ] ], "2": [ + [ + { + "id": "test_gbk" + }, + [ + + ] + ] + ], + "3": [ [ "BIGSLICE", "bigslice", @@ -41,6 +51,16 @@ "test.fa:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], + "tsv": [ + [ + { + "id": "test_gbk" + }, + [ + + ] + ] + ], "versions_bigslice": [ [ "BIGSLICE", @@ -63,12 +83,13 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-03-04T09:47:43.387153103" + "timestamp": "2026-03-24T13:30:09.301823884" }, "streptomyces_coelicolor - bigslice - gbk": { "content": [ "data.db", 40, + true, { "versions_bigslice": [ [ From bfedf4c2efcc871f21c52dc75684f644803d1333 Mon Sep 17 00:00:00 2001 From: SkyLexS Date: Tue, 24 Mar 2026 14:07:58 +0200 Subject: [PATCH 05/12] fixing versioning --- modules/nf-core/bigslice/main.nf | 2 +- modules/nf-core/bigslice/meta.yml | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/nf-core/bigslice/main.nf b/modules/nf-core/bigslice/main.nf index 3ce64c30649e..057d7f050e82 100644 --- a/modules/nf-core/bigslice/main.nf +++ b/modules/nf-core/bigslice/main.nf @@ -15,7 +15,7 @@ process BIGSLICE { tuple val(meta), path("${prefix}/result/data.db") , emit: db tuple val(meta), path("${prefix}/result/tmp/**/*.fa"), emit: fa tuple val(meta), path("${prefix}/result/tsv_export") , emit: tsv - tuple val("${task.process}"), val('bigslice'), eval("echo 2.0.2"), topic: versions, emit: versions_bigslice + tuple val("${task.process}"), val('bigslice'), val("2.0.2"), topic: versions, emit: versions_bigslice when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/bigslice/meta.yml b/modules/nf-core/bigslice/meta.yml index cf25e84ae773..c4b66c2777cd 100644 --- a/modules/nf-core/bigslice/meta.yml +++ b/modules/nf-core/bigslice/meta.yml @@ -80,7 +80,7 @@ output: description: The name of the tool - 2.0.2: type: string - description: The expression to obtain the version of the tool + description: The version of the tool topics: versions: @@ -92,7 +92,7 @@ topics: description: The name of the tool - 2.0.2: type: string - description: The expression to obtain the version of the tool + description: The version of the tool authors: - "@vagkaratzas" From f8542cae26561238ff27c559b33fda0baeaa9e8f Mon Sep 17 00:00:00 2001 From: SkyLexS Date: Wed, 1 Apr 2026 13:58:47 +0300 Subject: [PATCH 06/12] resolved export_tsv support and other parameters and fix parameter defaults --- modules/nf-core/bigslice/main.nf | 33 +++++++------ modules/nf-core/bigslice/meta.yml | 31 ++++++------ modules/nf-core/bigslice/tests/main.nf.test | 33 +++++++++++++ .../nf-core/bigslice/tests/main.nf.test.snap | 47 +++++++++++-------- 4 files changed, 94 insertions(+), 50 deletions(-) diff --git a/modules/nf-core/bigslice/main.nf b/modules/nf-core/bigslice/main.nf index 057d7f050e82..ffebb3f61ed2 100644 --- a/modules/nf-core/bigslice/main.nf +++ b/modules/nf-core/bigslice/main.nf @@ -10,11 +10,13 @@ process BIGSLICE { input: tuple val(meta), path(bgc, stageAs: 'bgc_files/*') path(hmmdb) + val(export_tsv) output: - tuple val(meta), path("${prefix}/result/data.db") , emit: db - tuple val(meta), path("${prefix}/result/tmp/**/*.fa"), emit: fa - tuple val(meta), path("${prefix}/result/tsv_export") , emit: tsv + tuple val(meta), path("${prefix}/data.db") , emit: db + tuple val(meta), path("${prefix}/tmp/**/*.fa"), emit: fa + tuple val(meta), path("${prefix}/tsv_export") , emit: tsv, optional: true + // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. tuple val("${task.process}"), val('bigslice'), val("2.0.2"), topic: versions, emit: versions_bigslice when: @@ -25,12 +27,7 @@ process BIGSLICE { def args2 = task.ext.args2 ?: '' prefix = task.ext.prefix ?: "${meta.id}" def sample = meta.id - def export_tsv_cmd = args2 ? """ - bigslice \\ - --export-tsv ${prefix}/result/tsv_export \\ - --program_db_folder ${hmmdb} \\ - ${prefix} - """ : '' + def export_tsv_cmd = export_tsv ? "bigslice --export-tsv ${prefix}/tsv_export --program_db_folder ${hmmdb} ${args2} ${prefix}" : '' """ mkdir -p input/dataset/${sample} input/taxonomy cp bgc_files/* input/dataset/${sample}/ @@ -47,23 +44,25 @@ process BIGSLICE { --program_db_folder ${hmmdb} \\ ${prefix} - mkdir -p ${prefix}/result/tsv_export ${export_tsv_cmd} + + mv ${prefix}/result/data.db ${prefix}/data.db + mv ${prefix}/result/tmp ${prefix}/tmp + rm -rf ${prefix}/result """ stub: def args = task.ext.args ?: '' - def args2 = task.ext.args2 ?: '' prefix = task.ext.prefix ?: "${meta.id}" """ echo ${args} - mkdir -p ${prefix}/result/tmp/2e555308dfc411186cf012334262f127 - mkdir -p ${prefix}/result/tsv_export - touch ${prefix}/result/data.db - touch ${prefix}/result/tmp/2e555308dfc411186cf012334262f127/test.fa - if [ -n "${args2}" ]; then - touch ${prefix}/result/tsv_export/bgcs.tsv + mkdir -p ${prefix}/tmp/2e555308dfc411186cf012334262f127 + touch ${prefix}/data.db + touch ${prefix}/tmp/2e555308dfc411186cf012334262f127/test.fa + if ${export_tsv}; then + mkdir -p ${prefix}/tsv_export + touch ${prefix}/tsv_export/bgcs.tsv fi """ } diff --git a/modules/nf-core/bigslice/meta.yml b/modules/nf-core/bigslice/meta.yml index c4b66c2777cd..354efa4a8460 100644 --- a/modules/nf-core/bigslice/meta.yml +++ b/modules/nf-core/bigslice/meta.yml @@ -8,15 +8,15 @@ keywords: - analysis tools: - "bigslice": - description: A highly scalable, user-interactive tool for the large scale analysis - of Biosynthetic Gene Clusters data + description: A highly scalable, user-interactive tool for the large scale + analysis of Biosynthetic Gene Clusters data homepage: "https://github.com/medema-group/bigslice" documentation: "https://github.com/medema-group/bigslice" tool_dev_url: "https://github.com/medema-group/bigslice" doi: "10.1093/gigascience/giaa154" - licence: ["AGPL v3-or-later"] + licence: + - "AGPL v3-or-later" identifier: "" - input: - - meta: type: map @@ -30,46 +30,51 @@ input: Each file represents a BGC region. The module internally organises them into the required BiG-SLiCE input folder structure (datasets.tsv and taxonomy TSV). pattern: "*.gbk" + ontologies: [] - hmmdb: type: directory description: | Path to the BiG-SLiCE HMM database folder containing biosynthetic and sub Pfams for annotation, in the required BiG-SLiCE format. An example directory in compressed archive format can be found here: https://github.com/medema-group/bigslice/releases/download/v2.0.0rc/bigslice-models.2022-11-30.tar.gz - + - export_tsv: + type: boolean + description: | + If true, runs a second BiG-SLiCE invocation to export all results from the SQLite database + to TSV files under `tsv_export/`. Additional arguments for this step can be passed via `task.ext.args2`. output: db: - - meta: type: map description: Groovy Map containing sample/dataset information - - ${prefix}/result/data.db: + - ${prefix}/data.db: type: file description: | The results SQLite database. Contains various tables relevant to result BGCs, CDSs, GCFs, HMMs and HSPs. pattern: "data.db" ontologies: - - edam: "http://edamontology.org/format_3621" # SQLite format + - edam: "http://edamontology.org/format_3621" fa: - - meta: type: map description: Groovy Map containing sample/dataset information - - ${prefix}/result/tmp/**/*.fa: + - ${prefix}/tmp/**/*.fa: type: file description: | Predicted features as FASTA files. One file per hit HMM. pattern: "*.fa" ontologies: - - edam: "http://edamontology.org/format_1929" # FASTA + - edam: "http://edamontology.org/format_1929" tsv: - - meta: type: map description: Groovy Map containing sample/dataset information - - ${prefix}/result/tsv_export: + - ${prefix}/tsv_export: type: directory description: | Directory containing TSV exports of all parsed BGC metadata, vectorized - features and clustering results. The directory is always created; files - are only present when `--export-tsv` is passed via `task.ext.args2`. + features and clustering results. Only present when `export_tsv` input is + set to `true`. Optional output. pattern: "tsv_export" versions_bigslice: - - ${task.process}: @@ -81,7 +86,6 @@ output: - 2.0.2: type: string description: The version of the tool - topics: versions: - - ${task.process}: @@ -93,7 +97,6 @@ topics: - 2.0.2: type: string description: The version of the tool - authors: - "@vagkaratzas" maintainers: diff --git a/modules/nf-core/bigslice/tests/main.nf.test b/modules/nf-core/bigslice/tests/main.nf.test index 08362ece6ee4..b9d9920e250a 100644 --- a/modules/nf-core/bigslice/tests/main.nf.test +++ b/modules/nf-core/bigslice/tests/main.nf.test @@ -67,6 +67,38 @@ nextflow_process { [ meta, gbk_files ] } input[1] = UNTAR_HMMDB.out.untar.map{ it -> it[1] } + input[2] = false + """ + } + } + + then { + assert process.success + assertAll( + { assert snapshot( + file(process.out.db[0][1]).name, + process.out.fa[0][1].size(), + process.out.tsv, + process.out.findAll { key, val -> key.startsWith("versions")} + ).match() } + ) + } + + } + + test("streptomyces_coelicolor - bigslice - gbk - export_tsv") { + + when { + process { + """ + // Flatten the GBK directory into a list of individual GBK files with meta + input[0] = UNTAR_GBK.out.untar.map { meta, dir -> + def gbk_files = [] + dir.eachFileRecurse { if (it.name.endsWith('.gbk')) gbk_files << it } + [ meta, gbk_files ] + } + input[1] = UNTAR_HMMDB.out.untar.map{ it -> it[1] } + input[2] = true """ } } @@ -99,6 +131,7 @@ nextflow_process { [ meta, gbk_files ] } input[1] = UNTAR_HMMDB.out.untar.map{ it -> it[1] } + input[2] = false """ } } diff --git a/modules/nf-core/bigslice/tests/main.nf.test.snap b/modules/nf-core/bigslice/tests/main.nf.test.snap index bb02cb917332..8af59978d610 100644 --- a/modules/nf-core/bigslice/tests/main.nf.test.snap +++ b/modules/nf-core/bigslice/tests/main.nf.test.snap @@ -1,4 +1,25 @@ { + "streptomyces_coelicolor - bigslice - gbk - export_tsv": { + "content": [ + "data.db", + 40, + true, + { + "versions_bigslice": [ + [ + "BIGSLICE", + "bigslice", + "2.0.2" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.3" + }, + "timestamp": "2026-04-01T12:36:35.604224477" + }, "streptomyces_coelicolor - bigslice - gbk - stub": { "content": [ { @@ -19,14 +40,7 @@ ] ], "2": [ - [ - { - "id": "test_gbk" - }, - [ - - ] - ] + ], "3": [ [ @@ -52,14 +66,7 @@ ] ], "tsv": [ - [ - { - "id": "test_gbk" - }, - [ - - ] - ] + ], "versions_bigslice": [ [ @@ -83,13 +90,15 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-03-24T13:30:09.301823884" + "timestamp": "2026-04-01T12:14:22.607521898" }, "streptomyces_coelicolor - bigslice - gbk": { "content": [ "data.db", 40, - true, + [ + + ], { "versions_bigslice": [ [ @@ -104,6 +113,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-03-04T09:47:30.918713387" + "timestamp": "2026-04-01T12:28:51.841331215" } } \ No newline at end of file From 4de6d518896a3f6e3f5de15ecc429ca81d261704 Mon Sep 17 00:00:00 2001 From: SkyLexS Date: Wed, 1 Apr 2026 16:10:26 +0300 Subject: [PATCH 07/12] collect all samples cross-run --- modules/nf-core/bigslice/main.nf | 24 ++- modules/nf-core/bigslice/meta.yml | 35 +--- modules/nf-core/bigslice/tests/main.nf.test | 26 ++- .../nf-core/bigslice/tests/main.nf.test.snap | 149 ++++++++++++++---- 4 files changed, 150 insertions(+), 84 deletions(-) diff --git a/modules/nf-core/bigslice/main.nf b/modules/nf-core/bigslice/main.nf index ffebb3f61ed2..58aa25c50b12 100644 --- a/modules/nf-core/bigslice/main.nf +++ b/modules/nf-core/bigslice/main.nf @@ -8,14 +8,12 @@ process BIGSLICE { : 'biocontainers/bigslice:2.0.2--pyh8ed023e_0'}" input: - tuple val(meta), path(bgc, stageAs: 'bgc_files/*') + tuple val(meta), path(bgc, stageAs: 'bgc_files/s*/*') path(hmmdb) val(export_tsv) output: - tuple val(meta), path("${prefix}/data.db") , emit: db - tuple val(meta), path("${prefix}/tmp/**/*.fa"), emit: fa - tuple val(meta), path("${prefix}/tsv_export") , emit: tsv, optional: true + tuple val(meta), path("${prefix}/result"), emit: output // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. tuple val("${task.process}"), val('bigslice'), val("2.0.2"), topic: versions, emit: versions_bigslice @@ -27,10 +25,10 @@ process BIGSLICE { def args2 = task.ext.args2 ?: '' prefix = task.ext.prefix ?: "${meta.id}" def sample = meta.id - def export_tsv_cmd = export_tsv ? "bigslice --export-tsv ${prefix}/tsv_export --program_db_folder ${hmmdb} ${args2} ${prefix}" : '' + def export_tsv_cmd = export_tsv ? "bigslice --export-tsv ${prefix}/result/tsv_export --program_db_folder ${hmmdb} ${args2} ${prefix}" : '' """ mkdir -p input/dataset/${sample} input/taxonomy - cp bgc_files/* input/dataset/${sample}/ + find bgc_files -name '*.gbk' | xargs -I{} cp {} input/dataset/${sample}/ printf "# dataset_name\\tdataset_path\\ttaxonomy_path\\tdescription\\n" > input/datasets.tsv printf "dataset\\tdataset\\ttaxonomy/taxonomy.tsv\\tBGC dataset\\n" >> input/datasets.tsv @@ -45,10 +43,6 @@ process BIGSLICE { ${prefix} ${export_tsv_cmd} - - mv ${prefix}/result/data.db ${prefix}/data.db - mv ${prefix}/result/tmp ${prefix}/tmp - rm -rf ${prefix}/result """ stub: @@ -57,12 +51,12 @@ process BIGSLICE { """ echo ${args} - mkdir -p ${prefix}/tmp/2e555308dfc411186cf012334262f127 - touch ${prefix}/data.db - touch ${prefix}/tmp/2e555308dfc411186cf012334262f127/test.fa + mkdir -p ${prefix}/result/tmp/2e555308dfc411186cf012334262f127 + touch ${prefix}/result/data.db + touch ${prefix}/result/tmp/2e555308dfc411186cf012334262f127/test.fa if ${export_tsv}; then - mkdir -p ${prefix}/tsv_export - touch ${prefix}/tsv_export/bgcs.tsv + mkdir -p ${prefix}/result/tsv_export + touch ${prefix}/result/tsv_export/bgcs.tsv fi """ } diff --git a/modules/nf-core/bigslice/meta.yml b/modules/nf-core/bigslice/meta.yml index 354efa4a8460..a668548d2c50 100644 --- a/modules/nf-core/bigslice/meta.yml +++ b/modules/nf-core/bigslice/meta.yml @@ -42,40 +42,17 @@ input: If true, runs a second BiG-SLiCE invocation to export all results from the SQLite database to TSV files under `tsv_export/`. Additional arguments for this step can be passed via `task.ext.args2`. output: - db: + output: - - meta: type: map description: Groovy Map containing sample/dataset information - - ${prefix}/data.db: - type: file - description: | - The results SQLite database. Contains various tables relevant to result - BGCs, CDSs, GCFs, HMMs and HSPs. - pattern: "data.db" - ontologies: - - edam: "http://edamontology.org/format_3621" - fa: - - - meta: - type: map - description: Groovy Map containing sample/dataset information - - ${prefix}/tmp/**/*.fa: - type: file - description: | - Predicted features as FASTA files. One file per hit HMM. - pattern: "*.fa" - ontologies: - - edam: "http://edamontology.org/format_1929" - tsv: - - - meta: - type: map - description: Groovy Map containing sample/dataset information - - ${prefix}/tsv_export: + - ${prefix}/result: type: directory description: | - Directory containing TSV exports of all parsed BGC metadata, vectorized - features and clustering results. Only present when `export_tsv` input is - set to `true`. Optional output. - pattern: "tsv_export" + BiG-SLiCE result directory containing the SQLite database (`data.db`), + predicted feature FASTA files (`tmp/**/*.fa`), and optionally TSV exports + (`tsv_export/`) when `export_tsv` is `true`. + pattern: "result" versions_bigslice: - - ${task.process}: type: string diff --git a/modules/nf-core/bigslice/tests/main.nf.test b/modules/nf-core/bigslice/tests/main.nf.test index b9d9920e250a..1e2af375dadd 100644 --- a/modules/nf-core/bigslice/tests/main.nf.test +++ b/modules/nf-core/bigslice/tests/main.nf.test @@ -74,11 +74,18 @@ nextflow_process { then { assert process.success + def stableFiles = [] + def unstableNames = [] + file(process.out.output[0][1]).eachFileRecurse { f -> + if (!f.isDirectory()) { + if (f.name.endsWith('.db')) { unstableNames.add(f.name) } + else { stableFiles.add(f) } + } + } assertAll( { assert snapshot( - file(process.out.db[0][1]).name, - process.out.fa[0][1].size(), - process.out.tsv, + stableFiles.sort { it.name }, + unstableNames.sort(), process.out.findAll { key, val -> key.startsWith("versions")} ).match() } ) @@ -105,11 +112,18 @@ nextflow_process { then { assert process.success + def stableFiles = [] + def unstableNames = [] + file(process.out.output[0][1]).eachFileRecurse { f -> + if (!f.isDirectory()) { + if (f.name.endsWith('.db')) { unstableNames.add(f.name) } + else { stableFiles.add(f) } + } + } assertAll( { assert snapshot( - file(process.out.db[0][1]).name, - process.out.fa[0][1].size(), - file(process.out.tsv[0][1]).isDirectory(), + stableFiles.sort { it.name }, + unstableNames.sort(), process.out.findAll { key, val -> key.startsWith("versions")} ).match() } ) diff --git a/modules/nf-core/bigslice/tests/main.nf.test.snap b/modules/nf-core/bigslice/tests/main.nf.test.snap index 8af59978d610..abf07050808e 100644 --- a/modules/nf-core/bigslice/tests/main.nf.test.snap +++ b/modules/nf-core/bigslice/tests/main.nf.test.snap @@ -1,9 +1,56 @@ { "streptomyces_coelicolor - bigslice - gbk - export_tsv": { "content": [ - "data.db", - 40, - true, + [ + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1111.fa:md5,7470c18519d81086b2c2ba924b4253ea", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1113.fa:md5,dc021a1b786f669f22ab375b2d1ca7a2", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1119.fa:md5,a616b59c6e51e8bae50be4fa7235532d", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1331.fa:md5,ec0ebd220c4ef9a21d3db1b9b4534eea", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1680.fa:md5,93f70c8a17ce608eabd22e1ac9109e8e", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1705.fa:md5,ceb9102e6cb1c9c08996a69f5252b4f5", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1715.fa:md5,b9cfb81277d916acbbaa4027ef9038dd", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1903.fa:md5,1df32de9f829b8bacf78f3458de3a9d4", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2047.fa:md5,20513daf3e05fe7ddadce3d16b231e56", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2048.fa:md5,f857fef67836630e41170dcee6b7fe12", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2049.fa:md5,b931dc958e51e3eba9af19f3c6a07428", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2053.fa:md5,1b286b9edb951a7c2bdbdecb228988ec", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2055.fa:md5,032637e43afa185f6828ad5754298e65", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2056.fa:md5,6fd664a9666761639949b28e341ce6f7", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2057.fa:md5,59366e5ec1341eb9481273f324c53c64", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2058.fa:md5,56a0ba191d0f53cdeaea9c042c3ef823", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2059.fa:md5,12c6e3b673041e8d3255a3b109cb3b2a", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2060.fa:md5,2a23a48eab3384b756fb56ef69341193", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2061.fa:md5,4ae638ad0da2b3cab10d8bc7d30f0662", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2062.fa:md5,8be0091c5c00a18fa105812bc0562925", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2064.fa:md5,2cfd2f544ad02ae6df3512f8aad8d2b8", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2164.fa:md5,e916ee30f4fe81ff1184d63a64dd73dd", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2232.fa:md5,fc730e537e3d1d2803a30e2d655a5ab6", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2233.fa:md5,93cc312426bfd62d5a0f2fb1ddbb5da8", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2238.fa:md5,20021a508b298d338516ec6a991d753b", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2264.fa:md5,1326738a2b0b61f08851c9523fe1069c", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_643.fa:md5,b3f94baa6320058ec3f1e3a13bd58103", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_665.fa:md5,a9a205b89684c3bb3bf50665c9f2720f", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_88.fa:md5,6ad3278dc4179fdcd4580f17bd040cdf", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1236.fa:md5,ce950a80f6e53746df27d026f4998181", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1237.fa:md5,4907aa7357a8ef24f32d85ae3f75e4ff", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1246.fa:md5,23cc0c67339d7229582622809fa44c2b", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1331.fa:md5,645b79cf9a8e8f9795fd12378ed8eaa5", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1631.fa:md5,bc9ee42dc229284251118143d27fcdf8", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_170.fa:md5,d1b318d269fd3e17cfa47c3a83f9cad1", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1848.fa:md5,db952b9ca377f66b349186cdee0d593b", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_2069.fa:md5,f741a2af8c09e66a592512619c507085", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_2070.fa:md5,0503f516745c5214ead48e65cc262f01", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_2321.fa:md5,6ea6a757a1bc2efa87b5a6987ee275a9", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_2322.fa:md5,0fe1eee95b57556e0afb3e7996b6f00d", + "bgc_features_1.pkl:md5,92769235a6738d6bf6788d25ba1c1277", + "bgc_metadata.tsv:md5,12952ce9b60d75f18a8289b2d6ac70da", + "gcf_membership.tsv:md5,64f80bdc85b76cdb844d534c22e7f0b2", + "gcf_models_1.pkl:md5,3e1583856baa1f250aaa131d928367ce", + "run_metadata.tsv:md5,13870c73bcc2e03c00d84247172dc6c1" + ], + [ + "data.db" + ], { "versions_bigslice": [ [ @@ -18,7 +65,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-04-01T12:36:35.604224477" + "timestamp": "2026-04-01T16:02:40.975838315" }, "streptomyces_coelicolor - bigslice - gbk - stub": { "content": [ @@ -28,45 +75,37 @@ { "id": "test_gbk" }, - "data.db:md5,d41d8cd98f00b204e9800998ecf8427e" + [ + "data.db:md5,d41d8cd98f00b204e9800998ecf8427e", + [ + [ + "test.fa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ] ] ], "1": [ - [ - { - "id": "test_gbk" - }, - "test.fa:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - - ], - "3": [ [ "BIGSLICE", "bigslice", "2.0.2" ] ], - "db": [ - [ - { - "id": "test_gbk" - }, - "data.db:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "fa": [ + "output": [ [ { "id": "test_gbk" }, - "test.fa:md5,d41d8cd98f00b204e9800998ecf8427e" + [ + "data.db:md5,d41d8cd98f00b204e9800998ecf8427e", + [ + [ + "test.fa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ] ] - ], - "tsv": [ - ], "versions_bigslice": [ [ @@ -90,14 +129,56 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-04-01T12:14:22.607521898" + "timestamp": "2026-04-01T15:24:06.894239399" }, "streptomyces_coelicolor - bigslice - gbk": { "content": [ - "data.db", - 40, [ - + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1111.fa:md5,7470c18519d81086b2c2ba924b4253ea", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1113.fa:md5,dc021a1b786f669f22ab375b2d1ca7a2", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1119.fa:md5,a616b59c6e51e8bae50be4fa7235532d", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1331.fa:md5,ec0ebd220c4ef9a21d3db1b9b4534eea", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1680.fa:md5,93f70c8a17ce608eabd22e1ac9109e8e", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1705.fa:md5,ceb9102e6cb1c9c08996a69f5252b4f5", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1715.fa:md5,b9cfb81277d916acbbaa4027ef9038dd", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1903.fa:md5,1df32de9f829b8bacf78f3458de3a9d4", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2047.fa:md5,20513daf3e05fe7ddadce3d16b231e56", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2048.fa:md5,f857fef67836630e41170dcee6b7fe12", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2049.fa:md5,b931dc958e51e3eba9af19f3c6a07428", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2053.fa:md5,1b286b9edb951a7c2bdbdecb228988ec", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2055.fa:md5,032637e43afa185f6828ad5754298e65", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2056.fa:md5,6fd664a9666761639949b28e341ce6f7", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2057.fa:md5,59366e5ec1341eb9481273f324c53c64", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2058.fa:md5,56a0ba191d0f53cdeaea9c042c3ef823", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2059.fa:md5,12c6e3b673041e8d3255a3b109cb3b2a", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2060.fa:md5,2a23a48eab3384b756fb56ef69341193", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2061.fa:md5,4ae638ad0da2b3cab10d8bc7d30f0662", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2062.fa:md5,8be0091c5c00a18fa105812bc0562925", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2064.fa:md5,2cfd2f544ad02ae6df3512f8aad8d2b8", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2164.fa:md5,e916ee30f4fe81ff1184d63a64dd73dd", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2232.fa:md5,fc730e537e3d1d2803a30e2d655a5ab6", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2233.fa:md5,93cc312426bfd62d5a0f2fb1ddbb5da8", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2238.fa:md5,20021a508b298d338516ec6a991d753b", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2264.fa:md5,1326738a2b0b61f08851c9523fe1069c", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_643.fa:md5,b3f94baa6320058ec3f1e3a13bd58103", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_665.fa:md5,a9a205b89684c3bb3bf50665c9f2720f", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_88.fa:md5,6ad3278dc4179fdcd4580f17bd040cdf", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1236.fa:md5,ce950a80f6e53746df27d026f4998181", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1237.fa:md5,4907aa7357a8ef24f32d85ae3f75e4ff", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1246.fa:md5,23cc0c67339d7229582622809fa44c2b", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1331.fa:md5,645b79cf9a8e8f9795fd12378ed8eaa5", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1631.fa:md5,bc9ee42dc229284251118143d27fcdf8", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_170.fa:md5,d1b318d269fd3e17cfa47c3a83f9cad1", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1848.fa:md5,db952b9ca377f66b349186cdee0d593b", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_2069.fa:md5,f741a2af8c09e66a592512619c507085", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_2070.fa:md5,0503f516745c5214ead48e65cc262f01", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_2321.fa:md5,6ea6a757a1bc2efa87b5a6987ee275a9", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_2322.fa:md5,0fe1eee95b57556e0afb3e7996b6f00d", + "bgc_features_1.pkl:md5,92769235a6738d6bf6788d25ba1c1277", + "gcf_models_1.pkl:md5,3e1583856baa1f250aaa131d928367ce" + ], + [ + "data.db" ], { "versions_bigslice": [ @@ -113,6 +194,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-04-01T12:28:51.841331215" + "timestamp": "2026-04-01T15:14:54.379420933" } } \ No newline at end of file From cbd886a0765312a17d88c267ab41c5ad8385a341 Mon Sep 17 00:00:00 2001 From: SkyLexS Date: Wed, 1 Apr 2026 16:32:47 +0300 Subject: [PATCH 08/12] updating snapshot --- modules/nf-core/bigslice/tests/main.nf.test.snap | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/bigslice/tests/main.nf.test.snap b/modules/nf-core/bigslice/tests/main.nf.test.snap index abf07050808e..a7c8835b9d49 100644 --- a/modules/nf-core/bigslice/tests/main.nf.test.snap +++ b/modules/nf-core/bigslice/tests/main.nf.test.snap @@ -46,7 +46,7 @@ "bgc_metadata.tsv:md5,12952ce9b60d75f18a8289b2d6ac70da", "gcf_membership.tsv:md5,64f80bdc85b76cdb844d534c22e7f0b2", "gcf_models_1.pkl:md5,3e1583856baa1f250aaa131d928367ce", - "run_metadata.tsv:md5,13870c73bcc2e03c00d84247172dc6c1" + "run_metadata.tsv:md5,3f4aeb10d4a605e9c6efda74bfd55008" ], [ "data.db" @@ -65,7 +65,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-04-01T16:02:40.975838315" + "timestamp": "2026-04-01T16:30:05.08141433" }, "streptomyces_coelicolor - bigslice - gbk - stub": { "content": [ From 59c156de2d6504c4ccf0eb50914fa336e33808fe Mon Sep 17 00:00:00 2001 From: SkyLexS Date: Wed, 1 Apr 2026 16:57:07 +0300 Subject: [PATCH 09/12] updating snapshot yet again --- modules/nf-core/bigslice/tests/main.nf.test | 14 +- .../nf-core/bigslice/tests/main.nf.test.snap | 179 +++++++++--------- 2 files changed, 100 insertions(+), 93 deletions(-) diff --git a/modules/nf-core/bigslice/tests/main.nf.test b/modules/nf-core/bigslice/tests/main.nf.test index 1e2af375dadd..29ad3cfa9dfe 100644 --- a/modules/nf-core/bigslice/tests/main.nf.test +++ b/modules/nf-core/bigslice/tests/main.nf.test @@ -78,8 +78,11 @@ nextflow_process { def unstableNames = [] file(process.out.output[0][1]).eachFileRecurse { f -> if (!f.isDirectory()) { - if (f.name.endsWith('.db')) { unstableNames.add(f.name) } - else { stableFiles.add(f) } + if (f.name.endsWith('.db') || f.name.endsWith('.fa') || f.name.endsWith('.pkl')) { + unstableNames.add(f.name) + } else { + stableFiles.add(f) + } } } assertAll( @@ -116,8 +119,11 @@ nextflow_process { def unstableNames = [] file(process.out.output[0][1]).eachFileRecurse { f -> if (!f.isDirectory()) { - if (f.name.endsWith('.db')) { unstableNames.add(f.name) } - else { stableFiles.add(f) } + if (f.name.endsWith('.db') || f.name.endsWith('.fa') || f.name.endsWith('.pkl')) { + unstableNames.add(f.name) + } else { + stableFiles.add(f) + } } } assertAll( diff --git a/modules/nf-core/bigslice/tests/main.nf.test.snap b/modules/nf-core/bigslice/tests/main.nf.test.snap index a7c8835b9d49..b3e6ffc187ca 100644 --- a/modules/nf-core/bigslice/tests/main.nf.test.snap +++ b/modules/nf-core/bigslice/tests/main.nf.test.snap @@ -2,54 +2,54 @@ "streptomyces_coelicolor - bigslice - gbk - export_tsv": { "content": [ [ - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1111.fa:md5,7470c18519d81086b2c2ba924b4253ea", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1113.fa:md5,dc021a1b786f669f22ab375b2d1ca7a2", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1119.fa:md5,a616b59c6e51e8bae50be4fa7235532d", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1331.fa:md5,ec0ebd220c4ef9a21d3db1b9b4534eea", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1680.fa:md5,93f70c8a17ce608eabd22e1ac9109e8e", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1705.fa:md5,ceb9102e6cb1c9c08996a69f5252b4f5", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1715.fa:md5,b9cfb81277d916acbbaa4027ef9038dd", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1903.fa:md5,1df32de9f829b8bacf78f3458de3a9d4", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2047.fa:md5,20513daf3e05fe7ddadce3d16b231e56", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2048.fa:md5,f857fef67836630e41170dcee6b7fe12", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2049.fa:md5,b931dc958e51e3eba9af19f3c6a07428", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2053.fa:md5,1b286b9edb951a7c2bdbdecb228988ec", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2055.fa:md5,032637e43afa185f6828ad5754298e65", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2056.fa:md5,6fd664a9666761639949b28e341ce6f7", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2057.fa:md5,59366e5ec1341eb9481273f324c53c64", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2058.fa:md5,56a0ba191d0f53cdeaea9c042c3ef823", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2059.fa:md5,12c6e3b673041e8d3255a3b109cb3b2a", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2060.fa:md5,2a23a48eab3384b756fb56ef69341193", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2061.fa:md5,4ae638ad0da2b3cab10d8bc7d30f0662", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2062.fa:md5,8be0091c5c00a18fa105812bc0562925", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2064.fa:md5,2cfd2f544ad02ae6df3512f8aad8d2b8", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2164.fa:md5,e916ee30f4fe81ff1184d63a64dd73dd", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2232.fa:md5,fc730e537e3d1d2803a30e2d655a5ab6", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2233.fa:md5,93cc312426bfd62d5a0f2fb1ddbb5da8", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2238.fa:md5,20021a508b298d338516ec6a991d753b", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2264.fa:md5,1326738a2b0b61f08851c9523fe1069c", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_643.fa:md5,b3f94baa6320058ec3f1e3a13bd58103", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_665.fa:md5,a9a205b89684c3bb3bf50665c9f2720f", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_88.fa:md5,6ad3278dc4179fdcd4580f17bd040cdf", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1236.fa:md5,ce950a80f6e53746df27d026f4998181", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1237.fa:md5,4907aa7357a8ef24f32d85ae3f75e4ff", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1246.fa:md5,23cc0c67339d7229582622809fa44c2b", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1331.fa:md5,645b79cf9a8e8f9795fd12378ed8eaa5", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1631.fa:md5,bc9ee42dc229284251118143d27fcdf8", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_170.fa:md5,d1b318d269fd3e17cfa47c3a83f9cad1", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1848.fa:md5,db952b9ca377f66b349186cdee0d593b", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_2069.fa:md5,f741a2af8c09e66a592512619c507085", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_2070.fa:md5,0503f516745c5214ead48e65cc262f01", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_2321.fa:md5,6ea6a757a1bc2efa87b5a6987ee275a9", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_2322.fa:md5,0fe1eee95b57556e0afb3e7996b6f00d", - "bgc_features_1.pkl:md5,92769235a6738d6bf6788d25ba1c1277", "bgc_metadata.tsv:md5,12952ce9b60d75f18a8289b2d6ac70da", "gcf_membership.tsv:md5,64f80bdc85b76cdb844d534c22e7f0b2", - "gcf_models_1.pkl:md5,3e1583856baa1f250aaa131d928367ce", - "run_metadata.tsv:md5,3f4aeb10d4a605e9c6efda74bfd55008" + "run_metadata.tsv:md5,d51a1997d61451043fbdc51ed0b35364" ], [ - "data.db" + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1111.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1113.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1119.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1331.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1680.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1705.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1715.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1903.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2047.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2048.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2049.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2053.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2055.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2056.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2057.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2058.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2059.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2060.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2061.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2062.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2064.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2164.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2232.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2233.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2238.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2264.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_643.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_665.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_88.fa", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1236.fa", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1237.fa", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1246.fa", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1331.fa", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1631.fa", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_170.fa", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1848.fa", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_2069.fa", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_2070.fa", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_2321.fa", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_2322.fa", + "bgc_features_1.pkl", + "data.db", + "gcf_models_1.pkl" ], { "versions_bigslice": [ @@ -65,7 +65,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-04-01T16:30:05.08141433" + "timestamp": "2026-04-01T16:54:59.453550526" }, "streptomyces_coelicolor - bigslice - gbk - stub": { "content": [ @@ -134,51 +134,52 @@ "streptomyces_coelicolor - bigslice - gbk": { "content": [ [ - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1111.fa:md5,7470c18519d81086b2c2ba924b4253ea", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1113.fa:md5,dc021a1b786f669f22ab375b2d1ca7a2", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1119.fa:md5,a616b59c6e51e8bae50be4fa7235532d", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1331.fa:md5,ec0ebd220c4ef9a21d3db1b9b4534eea", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1680.fa:md5,93f70c8a17ce608eabd22e1ac9109e8e", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1705.fa:md5,ceb9102e6cb1c9c08996a69f5252b4f5", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1715.fa:md5,b9cfb81277d916acbbaa4027ef9038dd", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1903.fa:md5,1df32de9f829b8bacf78f3458de3a9d4", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2047.fa:md5,20513daf3e05fe7ddadce3d16b231e56", - 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"bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2064.fa:md5,2cfd2f544ad02ae6df3512f8aad8d2b8", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2164.fa:md5,e916ee30f4fe81ff1184d63a64dd73dd", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2232.fa:md5,fc730e537e3d1d2803a30e2d655a5ab6", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2233.fa:md5,93cc312426bfd62d5a0f2fb1ddbb5da8", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2238.fa:md5,20021a508b298d338516ec6a991d753b", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2264.fa:md5,1326738a2b0b61f08851c9523fe1069c", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_643.fa:md5,b3f94baa6320058ec3f1e3a13bd58103", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_665.fa:md5,a9a205b89684c3bb3bf50665c9f2720f", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_88.fa:md5,6ad3278dc4179fdcd4580f17bd040cdf", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1236.fa:md5,ce950a80f6e53746df27d026f4998181", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1237.fa:md5,4907aa7357a8ef24f32d85ae3f75e4ff", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1246.fa:md5,23cc0c67339d7229582622809fa44c2b", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1331.fa:md5,645b79cf9a8e8f9795fd12378ed8eaa5", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1631.fa:md5,bc9ee42dc229284251118143d27fcdf8", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_170.fa:md5,d1b318d269fd3e17cfa47c3a83f9cad1", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1848.fa:md5,db952b9ca377f66b349186cdee0d593b", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_2069.fa:md5,f741a2af8c09e66a592512619c507085", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_2070.fa:md5,0503f516745c5214ead48e65cc262f01", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_2321.fa:md5,6ea6a757a1bc2efa87b5a6987ee275a9", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_2322.fa:md5,0fe1eee95b57556e0afb3e7996b6f00d", - "bgc_features_1.pkl:md5,92769235a6738d6bf6788d25ba1c1277", - "gcf_models_1.pkl:md5,3e1583856baa1f250aaa131d928367ce" + ], [ - "data.db" + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1111.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1113.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1119.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1331.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1680.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1705.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1715.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1903.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2047.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2048.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2049.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2053.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2055.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2056.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2057.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2058.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2059.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2060.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2061.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2062.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2064.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2164.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2232.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2233.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2238.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2264.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_643.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_665.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_88.fa", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1236.fa", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1237.fa", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1246.fa", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1331.fa", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1631.fa", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_170.fa", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1848.fa", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_2069.fa", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_2070.fa", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_2321.fa", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_2322.fa", + "bgc_features_1.pkl", + "data.db", + "gcf_models_1.pkl" ], { "versions_bigslice": [ @@ -194,6 +195,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-04-01T15:14:54.379420933" + "timestamp": "2026-04-01T16:53:47.742978831" } } \ No newline at end of file From eb1d391eac0e55a5c0de182477fa630dd762b5ab Mon Sep 17 00:00:00 2001 From: SkyLexS Date: Wed, 1 Apr 2026 17:19:02 +0300 Subject: [PATCH 10/12] updating snapshot --- modules/nf-core/bigslice/tests/main.nf.test | 34 ++---- .../nf-core/bigslice/tests/main.nf.test.snap | 102 +----------------- 2 files changed, 10 insertions(+), 126 deletions(-) diff --git a/modules/nf-core/bigslice/tests/main.nf.test b/modules/nf-core/bigslice/tests/main.nf.test index 29ad3cfa9dfe..cdc6b1575f27 100644 --- a/modules/nf-core/bigslice/tests/main.nf.test +++ b/modules/nf-core/bigslice/tests/main.nf.test @@ -74,21 +74,12 @@ nextflow_process { then { assert process.success - def stableFiles = [] - def unstableNames = [] - file(process.out.output[0][1]).eachFileRecurse { f -> - if (!f.isDirectory()) { - if (f.name.endsWith('.db') || f.name.endsWith('.fa') || f.name.endsWith('.pkl')) { - unstableNames.add(f.name) - } else { - stableFiles.add(f) - } - } - } + def resultDir = file(process.out.output[0][1]) assertAll( + { assert resultDir.isDirectory() }, + { assert file("${resultDir}/data.db").exists() }, + { assert resultDir.list().any { it.endsWith('.fa') || new File("${resultDir}/tmp").exists() } }, { assert snapshot( - stableFiles.sort { it.name }, - unstableNames.sort(), process.out.findAll { key, val -> key.startsWith("versions")} ).match() } ) @@ -115,21 +106,12 @@ nextflow_process { then { assert process.success - def stableFiles = [] - def unstableNames = [] - file(process.out.output[0][1]).eachFileRecurse { f -> - if (!f.isDirectory()) { - if (f.name.endsWith('.db') || f.name.endsWith('.fa') || f.name.endsWith('.pkl')) { - unstableNames.add(f.name) - } else { - stableFiles.add(f) - } - } - } + def resultDir = file(process.out.output[0][1]) assertAll( + { assert resultDir.isDirectory() }, + { assert file("${resultDir}/data.db").exists() }, + { assert file("${resultDir}/tsv_export").isDirectory() }, { assert snapshot( - stableFiles.sort { it.name }, - unstableNames.sort(), process.out.findAll { key, val -> key.startsWith("versions")} ).match() } ) diff --git a/modules/nf-core/bigslice/tests/main.nf.test.snap b/modules/nf-core/bigslice/tests/main.nf.test.snap index b3e6ffc187ca..2b13a7774b41 100644 --- a/modules/nf-core/bigslice/tests/main.nf.test.snap +++ b/modules/nf-core/bigslice/tests/main.nf.test.snap @@ -1,56 +1,6 @@ { "streptomyces_coelicolor - bigslice - gbk - export_tsv": { "content": [ - [ - "bgc_metadata.tsv:md5,12952ce9b60d75f18a8289b2d6ac70da", - "gcf_membership.tsv:md5,64f80bdc85b76cdb844d534c22e7f0b2", - "run_metadata.tsv:md5,d51a1997d61451043fbdc51ed0b35364" - ], - [ - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1111.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1113.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1119.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1331.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1680.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1705.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1715.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1903.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2047.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2048.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2049.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2053.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2055.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2056.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2057.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2058.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2059.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2060.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2061.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2062.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2064.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2164.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2232.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2233.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2238.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2264.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_643.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_665.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_88.fa", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1236.fa", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1237.fa", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1246.fa", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1331.fa", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1631.fa", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_170.fa", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1848.fa", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_2069.fa", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_2070.fa", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_2321.fa", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_2322.fa", - "bgc_features_1.pkl", - "data.db", - "gcf_models_1.pkl" - ], { "versions_bigslice": [ [ @@ -65,7 +15,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-04-01T16:54:59.453550526" + "timestamp": "2026-04-01T17:16:10.590236203" }, "streptomyces_coelicolor - bigslice - gbk - stub": { "content": [ @@ -133,54 +83,6 @@ }, "streptomyces_coelicolor - bigslice - gbk": { "content": [ - [ - - ], - [ - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1111.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1113.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1119.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1331.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1680.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1705.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1715.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1903.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2047.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2048.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2049.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2053.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2055.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2056.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2057.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2058.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2059.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2060.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2061.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2062.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2064.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2164.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2232.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2233.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2238.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2264.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_643.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_665.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_88.fa", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1236.fa", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1237.fa", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1246.fa", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1331.fa", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1631.fa", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_170.fa", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1848.fa", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_2069.fa", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_2070.fa", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_2321.fa", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_2322.fa", - "bgc_features_1.pkl", - "data.db", - "gcf_models_1.pkl" - ], { "versions_bigslice": [ [ @@ -195,6 +97,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-04-01T16:53:47.742978831" + "timestamp": "2026-04-01T17:12:56.092639244" } } \ No newline at end of file From 90fac067f5754555f9a4aaf6e0a5efc4aa597277 Mon Sep 17 00:00:00 2001 From: SkyLexS Date: Fri, 3 Apr 2026 00:41:09 +0300 Subject: [PATCH 11/12] add tsv emit, snapshot file names --- modules/nf-core/bigslice/main.nf | 3 +- modules/nf-core/bigslice/meta.yml | 13 +++ modules/nf-core/bigslice/tests/main.nf.test | 11 +- .../nf-core/bigslice/tests/main.nf.test.snap | 105 +++++++++++++++++- 4 files changed, 124 insertions(+), 8 deletions(-) diff --git a/modules/nf-core/bigslice/main.nf b/modules/nf-core/bigslice/main.nf index 58aa25c50b12..779095d6eaf7 100644 --- a/modules/nf-core/bigslice/main.nf +++ b/modules/nf-core/bigslice/main.nf @@ -13,7 +13,8 @@ process BIGSLICE { val(export_tsv) output: - tuple val(meta), path("${prefix}/result"), emit: output + tuple val(meta), path("${prefix}/result") , emit: output + tuple val(meta), path("${prefix}/result/tsv_export") , emit: tsv, optional: true // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. tuple val("${task.process}"), val('bigslice'), val("2.0.2"), topic: versions, emit: versions_bigslice diff --git a/modules/nf-core/bigslice/meta.yml b/modules/nf-core/bigslice/meta.yml index a668548d2c50..54caea097ad2 100644 --- a/modules/nf-core/bigslice/meta.yml +++ b/modules/nf-core/bigslice/meta.yml @@ -53,6 +53,17 @@ output: predicted feature FASTA files (`tmp/**/*.fa`), and optionally TSV exports (`tsv_export/`) when `export_tsv` is `true`. pattern: "result" + tsv: + - - meta: + type: map + description: Groovy Map containing sample/dataset information + - ${prefix}/result/tsv_export: + type: directory + description: | + Directory containing TSV exports of all parsed BGC metadata, vectorized + features and clustering results. Only present when `export_tsv` input is + set to `true`. + pattern: "tsv_export" versions_bigslice: - - ${task.process}: type: string @@ -76,5 +87,7 @@ topics: description: The version of the tool authors: - "@vagkaratzas" + - "@SkyLex" maintainers: - "@vagkaratzas" + - "@SkyLex" diff --git a/modules/nf-core/bigslice/tests/main.nf.test b/modules/nf-core/bigslice/tests/main.nf.test index cdc6b1575f27..192995ed8ad3 100644 --- a/modules/nf-core/bigslice/tests/main.nf.test +++ b/modules/nf-core/bigslice/tests/main.nf.test @@ -75,11 +75,12 @@ nextflow_process { then { assert process.success def resultDir = file(process.out.output[0][1]) + def allNames = [] + resultDir.eachFileRecurse { f -> if (!f.isDirectory()) allNames.add(f.name) } assertAll( { assert resultDir.isDirectory() }, - { assert file("${resultDir}/data.db").exists() }, - { assert resultDir.list().any { it.endsWith('.fa') || new File("${resultDir}/tmp").exists() } }, { assert snapshot( + allNames.sort(), process.out.findAll { key, val -> key.startsWith("versions")} ).match() } ) @@ -107,11 +108,13 @@ nextflow_process { then { assert process.success def resultDir = file(process.out.output[0][1]) + def allNames = [] + resultDir.eachFileRecurse { f -> if (!f.isDirectory()) allNames.add(f.name) } assertAll( { assert resultDir.isDirectory() }, - { assert file("${resultDir}/data.db").exists() }, - { assert file("${resultDir}/tsv_export").isDirectory() }, + { assert file(process.out.tsv[0][1]).isDirectory() }, { assert snapshot( + allNames.sort(), process.out.findAll { key, val -> key.startsWith("versions")} ).match() } ) diff --git a/modules/nf-core/bigslice/tests/main.nf.test.snap b/modules/nf-core/bigslice/tests/main.nf.test.snap index 2b13a7774b41..41df0f4823cf 100644 --- a/modules/nf-core/bigslice/tests/main.nf.test.snap +++ b/modules/nf-core/bigslice/tests/main.nf.test.snap @@ -1,6 +1,54 @@ { "streptomyces_coelicolor - bigslice - gbk - export_tsv": { "content": [ + [ + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1111.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1113.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1119.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1331.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1680.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1705.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1715.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1903.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2047.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2048.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2049.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2053.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2055.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2056.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2057.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2058.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2059.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2060.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2061.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2062.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2064.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2164.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2232.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2233.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2238.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2264.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_643.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_665.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_88.fa", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1236.fa", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1237.fa", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1246.fa", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1331.fa", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1631.fa", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_170.fa", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1848.fa", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_2069.fa", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_2070.fa", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_2321.fa", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_2322.fa", + "bgc_features_1.pkl", + "bgc_metadata.tsv", + "data.db", + "gcf_membership.tsv", + "gcf_models_1.pkl", + "run_metadata.tsv" + ], { "versions_bigslice": [ [ @@ -15,7 +63,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-04-01T17:16:10.590236203" + "timestamp": "2026-04-02T22:45:09.007296279" }, "streptomyces_coelicolor - bigslice - gbk - stub": { "content": [ @@ -36,6 +84,9 @@ ] ], "1": [ + + ], + "2": [ [ "BIGSLICE", "bigslice", @@ -56,6 +107,9 @@ ] ] ] + ], + "tsv": [ + ], "versions_bigslice": [ [ @@ -79,10 +133,55 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-04-01T15:24:06.894239399" + "timestamp": "2026-04-02T22:45:23.737040708" }, "streptomyces_coelicolor - bigslice - gbk": { "content": [ + [ + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1111.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1113.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1119.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1331.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1680.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1705.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1715.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1903.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2047.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2048.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2049.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2053.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2055.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2056.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2057.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2058.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2059.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2060.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2061.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2062.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2064.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2164.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2232.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2233.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2238.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2264.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_643.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_665.fa", + "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_88.fa", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1236.fa", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1237.fa", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1246.fa", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1331.fa", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1631.fa", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_170.fa", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1848.fa", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_2069.fa", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_2070.fa", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_2321.fa", + "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_2322.fa", + "bgc_features_1.pkl", + "data.db", + "gcf_models_1.pkl" + ], { "versions_bigslice": [ [ @@ -97,6 +196,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-04-01T17:12:56.092639244" + "timestamp": "2026-04-02T22:43:31.299832158" } } \ No newline at end of file From a3e6cb49d756837c1fc9e38a9f4d2a7872887b84 Mon Sep 17 00:00:00 2001 From: SkyLexS Date: Fri, 3 Apr 2026 01:19:00 +0300 Subject: [PATCH 12/12] updated tests --- modules/nf-core/bigslice/tests/main.nf.test | 26 +++++- .../nf-core/bigslice/tests/main.nf.test.snap | 84 +------------------ 2 files changed, 26 insertions(+), 84 deletions(-) diff --git a/modules/nf-core/bigslice/tests/main.nf.test b/modules/nf-core/bigslice/tests/main.nf.test index 192995ed8ad3..f895cfd0e01f 100644 --- a/modules/nf-core/bigslice/tests/main.nf.test +++ b/modules/nf-core/bigslice/tests/main.nf.test @@ -76,9 +76,20 @@ nextflow_process { assert process.success def resultDir = file(process.out.output[0][1]) def allNames = [] - resultDir.eachFileRecurse { f -> if (!f.isDirectory()) allNames.add(f.name) } + def tmpFaCount = 0 + resultDir.eachFileRecurse { f -> + if (!f.isDirectory()) { + def rel = resultDir.toPath().relativize(f.toPath()).toString() + if (rel.startsWith('tmp/') || rel.startsWith('tmp\\')) { + if (f.name.endsWith('.fa')) tmpFaCount++ + } else { + allNames.add(f.name) + } + } + } assertAll( { assert resultDir.isDirectory() }, + { assert tmpFaCount > 0 }, { assert snapshot( allNames.sort(), process.out.findAll { key, val -> key.startsWith("versions")} @@ -109,9 +120,20 @@ nextflow_process { assert process.success def resultDir = file(process.out.output[0][1]) def allNames = [] - resultDir.eachFileRecurse { f -> if (!f.isDirectory()) allNames.add(f.name) } + def tmpFaCount = 0 + resultDir.eachFileRecurse { f -> + if (!f.isDirectory()) { + def rel = resultDir.toPath().relativize(f.toPath()).toString() + if (rel.startsWith('tmp/') || rel.startsWith('tmp\\')) { + if (f.name.endsWith('.fa')) tmpFaCount++ + } else { + allNames.add(f.name) + } + } + } assertAll( { assert resultDir.isDirectory() }, + { assert tmpFaCount > 0 }, { assert file(process.out.tsv[0][1]).isDirectory() }, { assert snapshot( allNames.sort(), diff --git a/modules/nf-core/bigslice/tests/main.nf.test.snap b/modules/nf-core/bigslice/tests/main.nf.test.snap index 41df0f4823cf..d945a37e3ff2 100644 --- a/modules/nf-core/bigslice/tests/main.nf.test.snap +++ b/modules/nf-core/bigslice/tests/main.nf.test.snap @@ -2,46 +2,6 @@ "streptomyces_coelicolor - bigslice - gbk - export_tsv": { "content": [ [ - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1111.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1113.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1119.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1331.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1680.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1705.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1715.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1903.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2047.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2048.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2049.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2053.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2055.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2056.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2057.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2058.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2059.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2060.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2061.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2062.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2064.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2164.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2232.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2233.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2238.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2264.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_643.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_665.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_88.fa", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1236.fa", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1237.fa", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1246.fa", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1331.fa", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1631.fa", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_170.fa", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1848.fa", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_2069.fa", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_2070.fa", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_2321.fa", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_2322.fa", "bgc_features_1.pkl", "bgc_metadata.tsv", "data.db", @@ -63,7 +23,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-04-02T22:45:09.007296279" + "timestamp": "2026-04-03T01:11:26.257005672" }, "streptomyces_coelicolor - bigslice - gbk - stub": { "content": [ @@ -138,46 +98,6 @@ "streptomyces_coelicolor - bigslice - gbk": { "content": [ [ - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1111.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1113.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1119.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1331.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1680.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1705.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1715.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_1903.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2047.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2048.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2049.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2053.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2055.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2056.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2057.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2058.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2059.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2060.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2061.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2062.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2064.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2164.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2232.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2233.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2238.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_2264.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_643.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_665.fa", - "bgc_c4ca4238a0b923820dcc509a6f75849b_hmm_88.fa", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1236.fa", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1237.fa", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1246.fa", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1331.fa", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1631.fa", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_170.fa", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_1848.fa", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_2069.fa", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_2070.fa", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_2321.fa", - "bgc_c81e728d9d4c2f636f067f89cc14862c_hmm_2322.fa", "bgc_features_1.pkl", "data.db", "gcf_models_1.pkl" @@ -196,6 +116,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-04-02T22:43:31.299832158" + "timestamp": "2026-04-03T01:10:19.794409662" } } \ No newline at end of file