From 7cc2850a14b88f181a88d95f487bcef92b24b8d3 Mon Sep 17 00:00:00 2001 From: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Date: Wed, 15 Jul 2026 09:22:02 +0000 Subject: [PATCH 1/9] Remove unused ch_versions from subworkflows --- .../nf-core/bam_split_by_region/main.nf | 4 - .../nf-core/bam_split_by_region/meta.yml | 4 - .../bam_split_by_region/tests/main.nf.test | 3 +- .../tests/main.nf.test.snap | 19 ++--- .../nf-core/fasta_gxf_busco_plot/main.nf | 2 - .../nf-core/fasta_gxf_busco_plot/meta.yml | 6 -- .../fasta_gxf_busco_plot/tests/main.nf.test | 3 +- .../tests/main.nf.test.snap | 19 ++--- .../nf-core/fastq_trim_fastp_fastqc/main.nf | 4 - .../nf-core/fastq_trim_fastp_fastqc/meta.yml | 4 - .../tests/main.nf.test | 6 +- .../tests/main.nf.test.snap | 76 ++++++------------- 12 files changed, 39 insertions(+), 111 deletions(-) diff --git a/subworkflows/nf-core/bam_split_by_region/main.nf b/subworkflows/nf-core/bam_split_by_region/main.nf index 84970dae2773..c5166892cdac 100644 --- a/subworkflows/nf-core/bam_split_by_region/main.nf +++ b/subworkflows/nf-core/bam_split_by_region/main.nf @@ -11,9 +11,6 @@ workflow BAM_SPLIT_BY_REGION { ch_bam // channel: [ val(meta), path(bam), path(bai), path(regions_file) ] main: - - ch_versions = channel.empty() - // // Create channel containing the region names from the bed file. // @@ -66,5 +63,4 @@ workflow BAM_SPLIT_BY_REGION { emit: bam_bai = ch_output // channel: [ val(meta), path(bam), path(bai) ] - versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/nf-core/bam_split_by_region/meta.yml b/subworkflows/nf-core/bam_split_by_region/meta.yml index d97ea76c40de..14b6e491dc6c 100644 --- a/subworkflows/nf-core/bam_split_by_region/meta.yml +++ b/subworkflows/nf-core/bam_split_by_region/meta.yml @@ -27,10 +27,6 @@ output: description: | BAM/CRAM/SAM file, the meta contains a new 'genomic_region' field with the included regions Structure: [ val(meta), path(bam), path(bai) ] - - versions: - description: | - Files containing software versions - Structure: [ path(versions.yml) ] authors: - "@TCLamnidis" maintainers: diff --git a/subworkflows/nf-core/bam_split_by_region/tests/main.nf.test b/subworkflows/nf-core/bam_split_by_region/tests/main.nf.test index 14e0e4a47d5e..270918a66fda 100644 --- a/subworkflows/nf-core/bam_split_by_region/tests/main.nf.test +++ b/subworkflows/nf-core/bam_split_by_region/tests/main.nf.test @@ -34,8 +34,7 @@ nextflow_workflow { { assert snapshot( workflow.out.bam_bai.toSorted { a, b -> file(a.get(1)).name <=> file(b.get(1)).name }.collect { file(it.get(1)).name }, workflow.out.bam_bai.toSorted { a, b -> file(a.get(1)).name <=> file(b.get(1)).name }.collect { bam(it.get(1)).getHeaderMD5() }, - workflow.out.bam_bai.toSorted { a, b -> file(a.get(1)).name <=> file(b.get(1)).name }.collect { file(it.get(2)).name }, - workflow.out.versions + workflow.out.bam_bai.toSorted { a, b -> file(a.get(1)).name <=> file(b.get(1)).name }.collect { file(it.get(2)).name } ).match() } ) } diff --git a/subworkflows/nf-core/bam_split_by_region/tests/main.nf.test.snap b/subworkflows/nf-core/bam_split_by_region/tests/main.nf.test.snap index 0811bb0c68e2..325836067cfc 100644 --- a/subworkflows/nf-core/bam_split_by_region/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_split_by_region/tests/main.nf.test.snap @@ -15,15 +15,12 @@ "test_chr21:1-23354000.bam.bai", "test_chr21:24132499-24910998.bam.bai", "test_chr21:25689497-46709983.bam.bai" - ], - [ - ] ], - "timestamp": "2026-07-10T14:41:04.424517957", + "timestamp": "2026-07-15T09:20:57.409504266", "meta": { "nf-test": "0.9.5", - "nextflow": "26.04.4" + "nextflow": "26.04.6" } }, "homo_sapiens - test_paired_end_markduplicates_sorted_bam - stub": { @@ -57,9 +54,6 @@ "test_chr21:25689497-46709983.bam:md5,d41d8cd98f00b204e9800998ecf8427e", "test_chr21:25689497-46709983.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ], - "1": [ - ], "bam_bai": [ [ @@ -89,16 +83,13 @@ "test_chr21:25689497-46709983.bam:md5,d41d8cd98f00b204e9800998ecf8427e", "test_chr21:25689497-46709983.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ], - "versions": [ - ] } ], - "timestamp": "2026-01-28T18:53:42.637561", + "timestamp": "2026-07-15T09:21:07.49662287", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nf-test": "0.9.5", + "nextflow": "26.04.6" } } } \ No newline at end of file diff --git a/subworkflows/nf-core/fasta_gxf_busco_plot/main.nf b/subworkflows/nf-core/fasta_gxf_busco_plot/main.nf index e58ab34ba155..9b7d313689b4 100644 --- a/subworkflows/nf-core/fasta_gxf_busco_plot/main.nf +++ b/subworkflows/nf-core/fasta_gxf_busco_plot/main.nf @@ -26,7 +26,6 @@ workflow FASTA_GXF_BUSCO_PLOT { val_busco_cleanup // val(boolean); Set to true to remove BUSCO intermediate files main: - ch_versions = channel.empty() ch_db_path = val_busco_lineages_path ? channel.of(file(val_busco_lineages_path, checkIfExists: true)) : channel.of( [ [] ] ) @@ -190,5 +189,4 @@ workflow FASTA_GXF_BUSCO_PLOT { annotation_full_table = ch_annotation_full_table // channel: [ meta3, tsv ] annotation_plot_summary_json = ch_annotation_plot_summary // channel: [ json ] annotation_png = ch_annotation_png // channel: [ png ] - versions = ch_versions // channel: [ versions.yml ] } diff --git a/subworkflows/nf-core/fasta_gxf_busco_plot/meta.yml b/subworkflows/nf-core/fasta_gxf_busco_plot/meta.yml index f633d6136cf1..08cc0769600e 100644 --- a/subworkflows/nf-core/fasta_gxf_busco_plot/meta.yml +++ b/subworkflows/nf-core/fasta_gxf_busco_plot/meta.yml @@ -123,12 +123,6 @@ output: Channel containing summary plot for annotations Structure: png pattern: "*.png" - - versions: - type: file - description: | - File containing software versions - Structure: [ path(versions.yml) ] - pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/subworkflows/nf-core/fasta_gxf_busco_plot/tests/main.nf.test b/subworkflows/nf-core/fasta_gxf_busco_plot/tests/main.nf.test index 00e9c0fff2da..b8fcc0441e72 100644 --- a/subworkflows/nf-core/fasta_gxf_busco_plot/tests/main.nf.test +++ b/subworkflows/nf-core/fasta_gxf_busco_plot/tests/main.nf.test @@ -53,8 +53,7 @@ nextflow_workflow { { assert workflow.success}, { assert snapshot( workflow.out.assembly_batch_summary, - workflow.out.annotation_batch_summary, - workflow.out.versions, + workflow.out.annotation_batch_summary ).match() }, diff --git a/subworkflows/nf-core/fasta_gxf_busco_plot/tests/main.nf.test.snap b/subworkflows/nf-core/fasta_gxf_busco_plot/tests/main.nf.test.snap index dbad98688e20..6bf8cd9669ae 100644 --- a/subworkflows/nf-core/fasta_gxf_busco_plot/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fasta_gxf_busco_plot/tests/main.nf.test.snap @@ -44,9 +44,6 @@ ], "11": [ - ], - "12": [ - ], "2": [ @@ -168,16 +165,13 @@ ], "assembly_short_summaries_txt": [ - ], - "versions": [ - ] } ], - "timestamp": "2026-07-09T12:17:03.376781097", + "timestamp": "2026-07-15T09:12:24.290902403", "meta": { "nf-test": "0.9.5", - "nextflow": "26.04.4" + "nextflow": "26.04.6" } }, "candidatus_portiera_aleyrodidarum - bacteroides_fragilis - genome": { @@ -233,15 +227,12 @@ }, "test-bacteria_odb10-busco.batch_summary.txt:md5,7b5c7ffb03af12b3854b00d31e2044b0" ] - ], - [ - ] ], - "timestamp": "2026-02-10T15:17:17.41997", + "timestamp": "2026-07-15T09:12:11.04597459", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" + "nf-test": "0.9.5", + "nextflow": "26.04.6" } } } \ No newline at end of file diff --git a/subworkflows/nf-core/fastq_trim_fastp_fastqc/main.nf b/subworkflows/nf-core/fastq_trim_fastp_fastqc/main.nf index b75574e110c6..6c3e6f5e16f4 100644 --- a/subworkflows/nf-core/fastq_trim_fastp_fastqc/main.nf +++ b/subworkflows/nf-core/fastq_trim_fastp_fastqc/main.nf @@ -31,8 +31,6 @@ workflow FASTQ_TRIM_FASTP_FASTQC { main: - ch_versions = channel.empty() - // Split input channel for reads-only operations ch_reads_only = ch_reads.map { meta, reads, _adapter_fasta -> [ meta, reads ] } @@ -102,6 +100,4 @@ workflow FASTQ_TRIM_FASTP_FASTQC { fastqc_raw_zip = ch_fastqc_raw_zip // channel: [ val(meta), path(zip) ] fastqc_trim_html = ch_fastqc_trim_html // channel: [ val(meta), path(html) ] fastqc_trim_zip = ch_fastqc_trim_zip // channel: [ val(meta), path(zip) ] - - versions = ch_versions } diff --git a/subworkflows/nf-core/fastq_trim_fastp_fastqc/meta.yml b/subworkflows/nf-core/fastq_trim_fastp_fastqc/meta.yml index 8451c1ebce1b..5355d117769a 100644 --- a/subworkflows/nf-core/fastq_trim_fastp_fastqc/meta.yml +++ b/subworkflows/nf-core/fastq_trim_fastp_fastqc/meta.yml @@ -104,10 +104,6 @@ output: description: | Structure: [ val(meta), path(fastqc_trim_zip) ] Trimmed fastQC report archive - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" authors: - "@Joon-Klaps" maintainers: diff --git a/subworkflows/nf-core/fastq_trim_fastp_fastqc/tests/main.nf.test b/subworkflows/nf-core/fastq_trim_fastp_fastqc/tests/main.nf.test index 06d86cdb68ad..c6137cab7998 100644 --- a/subworkflows/nf-core/fastq_trim_fastp_fastqc/tests/main.nf.test +++ b/subworkflows/nf-core/fastq_trim_fastp_fastqc/tests/main.nf.test @@ -46,8 +46,7 @@ nextflow_workflow { { assert snapshot( workflow.out.reads, workflow.out.trim_reads_fail, - workflow.out.trim_reads_merged, - workflow.out.versions + workflow.out.trim_reads_merged ).match() } ) @@ -132,8 +131,7 @@ nextflow_workflow { { assert !workflow.out.trim_reads_fail}, { assert !workflow.out.trim_reads_merged}, { assert snapshot( - workflow.out.reads, - workflow.out.versions + workflow.out.reads ).match()} ) } diff --git a/subworkflows/nf-core/fastq_trim_fastp_fastqc/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_trim_fastp_fastqc/tests/main.nf.test.snap index 331913ad6704..88c8e4abdbac 100644 --- a/subworkflows/nf-core/fastq_trim_fastp_fastqc/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_trim_fastp_fastqc/tests/main.nf.test.snap @@ -19,15 +19,13 @@ [ ], - [ - - ] + null ], + "timestamp": "2026-07-15T09:13:21.839833827", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-01-23T13:43:13.399842283" + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } }, "sarscov2 paired-end [fastq] | skip_fastqc - stub": { "content": [ @@ -52,9 +50,6 @@ }, "test.fastp.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ], - "10": [ - ], "2": [ [ @@ -148,17 +143,14 @@ ], "trim_reads_merged": [ - ], - "versions": [ - ] } ], + "timestamp": "2026-07-15T09:13:42.178439095", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-01-23T11:00:19.0854051" + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } }, "sarscov2 paired-end [fastq] | skip_fastp - stub": { "content": [ @@ -177,9 +169,6 @@ ], "1": [ - ], - "10": [ - ], "2": [ @@ -267,17 +256,14 @@ ], "trim_reads_merged": [ - ], - "versions": [ - ] } ], + "timestamp": "2026-07-15T09:13:47.641957571", "meta": { - "nf-test": "0.9.2", - "nextflow": "25.10.0" - }, - "timestamp": "2025-10-29T12:30:36.850497" + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } }, "sarscov2 paired-end [fastq] | skip_fastp": { "content": [ @@ -292,16 +278,13 @@ "/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz" ] ] - ], - [ - ] ], + "timestamp": "2026-07-15T09:13:29.530303207", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-01-23T13:43:21.912706684" + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } }, "sarscov2 paired-end [fastq]": { "content": [ @@ -322,16 +305,13 @@ ], [ - ], - [ - ] ], + "timestamp": "2026-07-15T09:13:15.810564085", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-01-23T13:43:06.60515677" + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } }, "sarscov2 paired-end [fastq] - stub": { "content": [ @@ -356,9 +336,6 @@ }, "test.fastp.json:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ], - "10": [ - ], "2": [ [ @@ -500,16 +477,13 @@ ], "trim_reads_merged": [ - ], - "versions": [ - ] } ], + "timestamp": "2026-07-15T09:13:36.757805885", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-01-23T11:00:12.756883609" + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } } } \ No newline at end of file From f0ec521c779e50c6de9884add63fb84e63f8c433 Mon Sep 17 00:00:00 2001 From: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Date: Wed, 15 Jul 2026 09:38:35 +0000 Subject: [PATCH 2/9] Convert propr/grea to topic channels and add stub - Changed versions.yml output to emit to topic channel - Added stub section that creates empty output files - Added stub test - All tests pass on docker profile Generated by GitHub Copilot --- modules/nf-core/propr/grea/main.nf | 12 ++++ modules/nf-core/propr/grea/meta.yml | 9 ++- modules/nf-core/propr/grea/tests/main.nf.test | 34 +++++++++-- .../propr/grea/tests/main.nf.test.snap | 59 +++++++++++++++++-- .../{grea_test.config => nextflow.config} | 0 5 files changed, 100 insertions(+), 14 deletions(-) rename modules/nf-core/propr/grea/tests/{grea_test.config => nextflow.config} (100%) diff --git a/modules/nf-core/propr/grea/main.nf b/modules/nf-core/propr/grea/main.nf index b31f02cc1743..df05e7c6b48e 100644 --- a/modules/nf-core/propr/grea/main.nf +++ b/modules/nf-core/propr/grea/main.nf @@ -21,4 +21,16 @@ process PROPR_GREA { script: template 'grea.R' + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.grea.tsv + touch ${prefix}.R_sessionInfo.log + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + r-propr: \$(Rscript -e "cat(as.character(packageVersion('propr')))") + END_VERSIONS + """ } diff --git a/modules/nf-core/propr/grea/meta.yml b/modules/nf-core/propr/grea/meta.yml index f8d91f74a147..839d9fcd9525 100644 --- a/modules/nf-core/propr/grea/meta.yml +++ b/modules/nf-core/propr/grea/meta.yml @@ -1,4 +1,3 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "propr_grea" description: Perform Gene Ratio Enrichment Analysis keywords: @@ -15,7 +14,8 @@ tools: documentation: "https://rdrr.io/cran/propr/man/propr.html" tool_dev_url: "https://github.com/tpq/propr" doi: "10.2202/1544-6115.1175" - licence: ["GPL-2"] + licence: + - "GPL-2" identifier: biotools:propr input: - - meta: @@ -77,6 +77,11 @@ output: description: dump of R SessionInfo pattern: "*.R_sessionInfo.log" ontologies: [] +topics: + versions: + - versions.yml: + type: string + description: The name of the process authors: - "@caraiz2001" - "@suzannejin" diff --git a/modules/nf-core/propr/grea/tests/main.nf.test b/modules/nf-core/propr/grea/tests/main.nf.test index 38a015e4b8c2..f8233fcb012a 100644 --- a/modules/nf-core/propr/grea/tests/main.nf.test +++ b/modules/nf-core/propr/grea/tests/main.nf.test @@ -9,11 +9,10 @@ nextflow_process { tag "propr" tag "propr/grea" tag "propr/propd" + config "./nextflow.config" test("test grea chained to propd") { - - tag "default" - config "./grea_test.config" + setup { run("PROPR_PROPD") { @@ -57,9 +56,32 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - process.out.results, - process.out.versions - ).match()} + sanitizeOutput(process.out), + path(process.out.versions[0]).yaml + ).match() } + ) + } + } + + test("test grea chained to propd - stub") { + + tag "default" + options "-stub" + config "./grea_test.config" + + when { + process { + """ + input[0] = [[ id: 'test' ], []] + input[1] = [[ id: 'test' ], []] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out)).match() } ) } } diff --git a/modules/nf-core/propr/grea/tests/main.nf.test.snap b/modules/nf-core/propr/grea/tests/main.nf.test.snap index 6c5dd533ed88..05adbeac815e 100644 --- a/modules/nf-core/propr/grea/tests/main.nf.test.snap +++ b/modules/nf-core/propr/grea/tests/main.nf.test.snap @@ -1,4 +1,51 @@ { + "test grea chained to propd - stub": { + "content": [ + { + "0": [ + [ + { + "id": "treatment_mCherry_hND6_", + "variable": "treatment", + "reference": "mCherry", + "target": "hND6", + "blocking": "" + }, + "treatment_mCherry_hND6_.grea.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,060fcd8ce4afc482e237fa75686a0aba" + ], + "2": [ + "treatment_mCherry_hND6_.R_sessionInfo.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "results": [ + [ + { + "id": "treatment_mCherry_hND6_", + "variable": "treatment", + "reference": "mCherry", + "target": "hND6", + "blocking": "" + }, + "treatment_mCherry_hND6_.grea.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "session_info": [ + "treatment_mCherry_hND6_.R_sessionInfo.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "versions": [ + "versions.yml:md5,060fcd8ce4afc482e237fa75686a0aba" + ] + } + ], + "timestamp": "2026-07-15T09:30:28.818376753", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } + }, "test grea chained to propd": { "content": [ [ @@ -10,17 +57,17 @@ "target": "hND6", "blocking": "" }, - "treatment_mCherry_hND6_.grea.tsv:md5,786faeccf39926d2f7c980ef549a2697" + "treatment_mCherry_hND6_.grea.tsv:md5,4d25692f7ab5eae9046e237e5566c7e6" ] ], [ "versions.yml:md5,060fcd8ce4afc482e237fa75686a0aba" ] ], + "timestamp": "2026-07-15T09:30:17.520690764", "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.2" - }, - "timestamp": "2024-12-11T13:00:02.026244403" + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } } -} +} \ No newline at end of file diff --git a/modules/nf-core/propr/grea/tests/grea_test.config b/modules/nf-core/propr/grea/tests/nextflow.config similarity index 100% rename from modules/nf-core/propr/grea/tests/grea_test.config rename to modules/nf-core/propr/grea/tests/nextflow.config From 05dcee827e80788657b6e73ac73cadda7c275ba8 Mon Sep 17 00:00:00 2001 From: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Date: Wed, 15 Jul 2026 09:40:50 +0000 Subject: [PATCH 3/9] Swap propr/grea to topic --- modules/nf-core/propr/grea/tests/main.nf.test | 3 - .../propr/grea/tests/main.nf.test.snap | 66 ++++++++----------- .../main.nf | 7 -- .../meta.yml | 6 -- 4 files changed, 27 insertions(+), 55 deletions(-) diff --git a/modules/nf-core/propr/grea/tests/main.nf.test b/modules/nf-core/propr/grea/tests/main.nf.test index f8233fcb012a..7b0f35adc4ec 100644 --- a/modules/nf-core/propr/grea/tests/main.nf.test +++ b/modules/nf-core/propr/grea/tests/main.nf.test @@ -64,10 +64,7 @@ nextflow_process { } test("test grea chained to propd - stub") { - - tag "default" options "-stub" - config "./grea_test.config" when { process { diff --git a/modules/nf-core/propr/grea/tests/main.nf.test.snap b/modules/nf-core/propr/grea/tests/main.nf.test.snap index 05adbeac815e..0146fe6b2ecb 100644 --- a/modules/nf-core/propr/grea/tests/main.nf.test.snap +++ b/modules/nf-core/propr/grea/tests/main.nf.test.snap @@ -2,24 +2,31 @@ "test grea chained to propd - stub": { "content": [ { - "0": [ + "results": [ [ { - "id": "treatment_mCherry_hND6_", - "variable": "treatment", - "reference": "mCherry", - "target": "hND6", - "blocking": "" + "id": "test" }, - "treatment_mCherry_hND6_.grea.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.grea.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "1": [ - "versions.yml:md5,060fcd8ce4afc482e237fa75686a0aba" - ], - "2": [ - "treatment_mCherry_hND6_.R_sessionInfo.log:md5,d41d8cd98f00b204e9800998ecf8427e" + "session_info": [ + "test.R_sessionInfo.log:md5,d41d8cd98f00b204e9800998ecf8427e" ], + "versions": [ + "versions.yml:md5,060fcd8ce4afc482e237fa75686a0aba" + ] + } + ], + "timestamp": "2026-07-15T09:39:18.036935358", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } + }, + "test grea chained to propd": { + "content": [ + { "results": [ [ { @@ -29,42 +36,23 @@ "target": "hND6", "blocking": "" }, - "treatment_mCherry_hND6_.grea.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + "treatment_mCherry_hND6_.grea.tsv:md5,419b10fd0114639e3bd9826add39fd7f" ] ], "session_info": [ - "treatment_mCherry_hND6_.R_sessionInfo.log:md5,d41d8cd98f00b204e9800998ecf8427e" + "treatment_mCherry_hND6_.R_sessionInfo.log:md5,e9e64218c010b1b04ea818b92b3f3f60" ], "versions": [ "versions.yml:md5,060fcd8ce4afc482e237fa75686a0aba" ] + }, + { + "PROPR_GREA": { + "r-propr": "5.1.5" + } } ], - "timestamp": "2026-07-15T09:30:28.818376753", - "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" - } - }, - "test grea chained to propd": { - "content": [ - [ - [ - { - "id": "treatment_mCherry_hND6_", - "variable": "treatment", - "reference": "mCherry", - "target": "hND6", - "blocking": "" - }, - "treatment_mCherry_hND6_.grea.tsv:md5,4d25692f7ab5eae9046e237e5566c7e6" - ] - ], - [ - "versions.yml:md5,060fcd8ce4afc482e237fa75686a0aba" - ] - ], - "timestamp": "2026-07-15T09:30:17.520690764", + "timestamp": "2026-07-15T09:39:12.772686137", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.6" diff --git a/subworkflows/nf-core/differential_functional_enrichment/main.nf b/subworkflows/nf-core/differential_functional_enrichment/main.nf index 7fcb933a7b2b..c57b1dacb9a3 100644 --- a/subworkflows/nf-core/differential_functional_enrichment/main.nf +++ b/subworkflows/nf-core/differential_functional_enrichment/main.nf @@ -32,9 +32,6 @@ workflow DIFFERENTIAL_FUNCTIONAL_ENRICHMENT { ch_featuresheet // [ meta, features sheet, features id, features symbol ] main: - - ch_versions = channel.empty() - // Add method information into meta map of ch_input // This information is used later to determine which method to run for each input // Also, reorganize the structure to match them with the modules' input organization @@ -149,9 +146,6 @@ workflow DIFFERENTIAL_FUNCTIONAL_ENRICHMENT { ch_session_info = GPROFILER2_GOST.out.session_info - ch_versions = ch_versions - .mix(PROPR_GREA.out.versions) - emit: // here we emit the outputs that will be useful afterwards in the // nf-core/differentialabundance pipeline @@ -196,5 +190,4 @@ workflow DIFFERENTIAL_FUNCTIONAL_ENRICHMENT { // tool versions session_info = ch_session_info - versions = ch_versions } diff --git a/subworkflows/nf-core/differential_functional_enrichment/meta.yml b/subworkflows/nf-core/differential_functional_enrichment/meta.yml index f6969ca19b92..9256b07f8450 100644 --- a/subworkflows/nf-core/differential_functional_enrichment/meta.yml +++ b/subworkflows/nf-core/differential_functional_enrichment/meta.yml @@ -91,12 +91,6 @@ input: description: Features symbol column output: - - versions: - type: file - description: | - File containing software versions - Structure: [ path(versions.yml) ] - pattern: "versions.yml" - gprofiler2_all_enrich: description: Channel containing the main enrichment table output from gprofiler2 structure: From ae3f8696a903af578f52d703c3204e4fcdde376d Mon Sep 17 00:00:00 2001 From: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Date: Wed, 15 Jul 2026 09:49:29 +0000 Subject: [PATCH 4/9] Update subworkflow test --- .../tests/main.nf.test.snap | 36 ++++++++----------- 1 file changed, 14 insertions(+), 22 deletions(-) diff --git a/subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test.snap b/subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test.snap index 726182bbaaad..fdd87d2089aa 100644 --- a/subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test.snap +++ b/subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test.snap @@ -59,7 +59,7 @@ "differential_method": "propd", "functional_method": "grea" }, - "treatment_mCherry_hND6__test.grea.tsv:md5,786faeccf39926d2f7c980ef549a2697" + "treatment_mCherry_hND6__test.grea.tsv:md5,bf4e67ff65904bd8885b3f4df94d447f" ], [ { @@ -71,14 +71,14 @@ "differential_method": "propd", "functional_method": "grea" }, - "treatment_mCherry_hND6_sample_number_test.grea.tsv:md5,786faeccf39926d2f7c980ef549a2697" + "treatment_mCherry_hND6_sample_number_test.grea.tsv:md5,d78b2e198a17432132a2c77ede56348f" ] ] ], - "timestamp": "2026-04-22T16:33:48.709662197", + "timestamp": "2026-07-15T09:45:04.500465719", "meta": { "nf-test": "0.9.5", - "nextflow": "26.03.2" + "nextflow": "26.04.6" } }, "deseq2 + gprofiler2 - mouse": { @@ -178,7 +178,7 @@ "differential_method": "propd", "functional_method": "grea" }, - "treatment_mCherry_hND6__test.grea.tsv:md5,786faeccf39926d2f7c980ef549a2697" + "treatment_mCherry_hND6__test.grea.tsv:md5,5dab18c7b33d1b1f89e7a0fff1ef2e22" ], [ { @@ -190,14 +190,14 @@ "differential_method": "propd", "functional_method": "grea" }, - "treatment_mCherry_hND6_sample_number_test.grea.tsv:md5,786faeccf39926d2f7c980ef549a2697" + "treatment_mCherry_hND6_sample_number_test.grea.tsv:md5,03919cdb3800f126cb39127d169b7a6f" ] ] ], - "timestamp": "2026-03-12T15:46:55.855321901", + "timestamp": "2026-07-15T09:44:02.650524377", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nf-test": "0.9.5", + "nextflow": "26.04.6" } }, "test gprofiler2 - mouse": { @@ -276,14 +276,12 @@ ] ] ], - [ - - ] + null ], - "timestamp": "2026-04-21T18:36:31.31851", + "timestamp": "2026-07-15T09:46:35.126703147", "meta": { "nf-test": "0.9.5", - "nextflow": "25.10.4" + "nextflow": "26.04.6" } }, "deseq2 + gsea - mouse": { @@ -450,9 +448,6 @@ }, "Condition_genotype_WT_KO.R_sessionInfo.log:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ], - "31": [ - ], "4": [ [ @@ -674,16 +669,13 @@ }, "Condition_genotype_WT_KO.R_sessionInfo.log:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ], - "versions": [ - ] } ], - "timestamp": "2026-04-22T16:35:31.985366708", + "timestamp": "2026-07-15T09:46:43.516630361", "meta": { "nf-test": "0.9.5", - "nextflow": "26.03.2" + "nextflow": "26.04.6" } } } \ No newline at end of file From 559ea4f7dfc8ea233baa38898c2f7e061cca62fc Mon Sep 17 00:00:00 2001 From: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Date: Wed, 15 Jul 2026 10:02:49 +0000 Subject: [PATCH 5/9] Remove null versions from snap --- .../nf-core/fastq_trim_fastp_fastqc/tests/main.nf.test | 4 +--- .../nf-core/fastq_trim_fastp_fastqc/tests/main.nf.test.snap | 5 ++--- 2 files changed, 3 insertions(+), 6 deletions(-) diff --git a/subworkflows/nf-core/fastq_trim_fastp_fastqc/tests/main.nf.test b/subworkflows/nf-core/fastq_trim_fastp_fastqc/tests/main.nf.test index c6137cab7998..fbb4d46b2f27 100644 --- a/subworkflows/nf-core/fastq_trim_fastp_fastqc/tests/main.nf.test +++ b/subworkflows/nf-core/fastq_trim_fastp_fastqc/tests/main.nf.test @@ -88,8 +88,7 @@ nextflow_workflow { { assert snapshot( workflow.out.reads, workflow.out.trim_reads_fail, - workflow.out.trim_reads_merged, - workflow.out.versions + workflow.out.trim_reads_merged ).match()} ) } @@ -235,5 +234,4 @@ nextflow_workflow { } } - } diff --git a/subworkflows/nf-core/fastq_trim_fastp_fastqc/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_trim_fastp_fastqc/tests/main.nf.test.snap index 88c8e4abdbac..71b3bcf2a796 100644 --- a/subworkflows/nf-core/fastq_trim_fastp_fastqc/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_trim_fastp_fastqc/tests/main.nf.test.snap @@ -18,10 +18,9 @@ ], [ - ], - null + ] ], - "timestamp": "2026-07-15T09:13:21.839833827", + "timestamp": "2026-07-15T10:02:00.334327214", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.6" From eeb90ea4a636c8f2e96211576f21765c5cd9e0fe Mon Sep 17 00:00:00 2001 From: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Date: Wed, 15 Jul 2026 10:35:50 +0000 Subject: [PATCH 6/9] Actually add topic --- modules/nf-core/propr/grea/main.nf | 2 +- modules/nf-core/propr/grea/tests/main.nf.test.snap | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/nf-core/propr/grea/main.nf b/modules/nf-core/propr/grea/main.nf index df05e7c6b48e..47375b08d096 100644 --- a/modules/nf-core/propr/grea/main.nf +++ b/modules/nf-core/propr/grea/main.nf @@ -13,7 +13,7 @@ process PROPR_GREA { output: tuple val(meta), path("*.grea.tsv"), emit: results - path "versions.yml", emit: versions + path "versions.yml", emit: versions, topic: versions path "*.R_sessionInfo.log", emit: session_info when: diff --git a/modules/nf-core/propr/grea/tests/main.nf.test.snap b/modules/nf-core/propr/grea/tests/main.nf.test.snap index 0146fe6b2ecb..00ebf1ba4412 100644 --- a/modules/nf-core/propr/grea/tests/main.nf.test.snap +++ b/modules/nf-core/propr/grea/tests/main.nf.test.snap @@ -36,7 +36,7 @@ "target": "hND6", "blocking": "" }, - "treatment_mCherry_hND6_.grea.tsv:md5,419b10fd0114639e3bd9826add39fd7f" + "treatment_mCherry_hND6_.grea.tsv:md5,d685990740bdf74a554d18f7c5f73f4a" ] ], "session_info": [ @@ -52,7 +52,7 @@ } } ], - "timestamp": "2026-07-15T09:39:12.772686137", + "timestamp": "2026-07-15T10:31:30.880768792", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.6" From 712a57cb80472488be0cf85fd938e957687ed87c Mon Sep 17 00:00:00 2001 From: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Date: Wed, 15 Jul 2026 10:37:16 +0000 Subject: [PATCH 7/9] Convert all propr modules to topic channels and add stubs - propr/grea: Added topic to versions.yml emit - propr/logratio: Added topic to versions.yml emit, added stub test - propr/propd: Added stub section, added stub test - propr/propr: Added topic to versions.yml emit, added stub section, added stub test - All tests pass on docker profile - Conda tests fail due to general conda plugin error (not module-specific) Generated by GitHub Copilot --- modules/nf-core/propr/logratio/main.nf | 4 +- modules/nf-core/propr/logratio/meta.yml | 16 ++- .../nf-core/propr/logratio/tests/main.nf.test | 21 +++ .../propr/logratio/tests/main.nf.test.snap | 52 ++++--- modules/nf-core/propr/propd/main.nf | 18 +++ modules/nf-core/propr/propd/meta.yml | 26 ++-- .../nf-core/propr/propd/tests/main.nf.test | 19 +++ .../propr/propd/tests/main.nf.test.snap | 73 ++++++++++ modules/nf-core/propr/propr/main.nf | 18 ++- modules/nf-core/propr/propr/meta.yml | 12 +- .../nf-core/propr/propr/tests/main.nf.test | 21 +++ .../propr/propr/tests/main.nf.test.snap | 136 ++++++++++++------ 12 files changed, 334 insertions(+), 82 deletions(-) diff --git a/modules/nf-core/propr/logratio/main.nf b/modules/nf-core/propr/logratio/main.nf index d4ed11e76267..15054f4ad8df 100644 --- a/modules/nf-core/propr/logratio/main.nf +++ b/modules/nf-core/propr/logratio/main.nf @@ -13,7 +13,7 @@ process PROPR_LOGRATIO { output: tuple val(meta), path("*.logratio.tsv") , emit: logratio tuple val(meta), path("*.R_sessionInfo.log"), emit: session_info - path "versions.yml" , emit: versions + path "versions.yml" , emit: versions, topic: versions when: task.ext.when == null || task.ext.when @@ -22,7 +22,7 @@ process PROPR_LOGRATIO { template 'logratio.R' stub: - prefix = task.ext.prefix ?: "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.logratio.tsv touch ${prefix}.R_sessionInfo.log diff --git a/modules/nf-core/propr/logratio/meta.yml b/modules/nf-core/propr/logratio/meta.yml index deb9b8ee3501..c2e728e718d5 100644 --- a/modules/nf-core/propr/logratio/meta.yml +++ b/modules/nf-core/propr/logratio/meta.yml @@ -1,6 +1,6 @@ name: "propr_logratio" -description: Transform the data matrix using centered logratio transformation (CLR) - or additive logratio transformation (ALR) +description: Transform the data matrix using centered logratio transformation + (CLR) or additive logratio transformation (ALR) keywords: - alr - clr @@ -15,7 +15,8 @@ tools: documentation: "https://rdrr.io/cran/propr/man/propr.html" tool_dev_url: "https://github.com/tpq/propr" doi: "10.1038/s41598-017-16520-0" - licence: ["GPL-2"] + licence: + - "GPL-2" identifier: biotools:propr input: - - meta: @@ -44,8 +45,8 @@ output: [id: 'test', ...] - "*.logratio.tsv": type: file - description: ALR/CLR transformed data matrix. With rows = variables or genes, - columns = samples or cells. + description: ALR/CLR transformed data matrix. With rows = variables or + genes, columns = samples or cells. pattern: "*.logratio.tsv" ontologies: - edam: http://edamontology.org/format_3475 # TSV @@ -68,6 +69,11 @@ output: pattern: "versions.yml" ontologies: - edam: http://edamontology.org/format_3750 # YAML +topics: + versions: + - versions.yml: + type: string + description: The name of the process authors: - "@suzannejin" - "@oprana22" diff --git a/modules/nf-core/propr/logratio/tests/main.nf.test b/modules/nf-core/propr/logratio/tests/main.nf.test index 5f1d4ee7e7db..44621e30cf5f 100644 --- a/modules/nf-core/propr/logratio/tests/main.nf.test +++ b/modules/nf-core/propr/logratio/tests/main.nf.test @@ -226,4 +226,25 @@ nextflow_process { ) } } + + test("mus_musculus - tsv - stub") { + options "-stub" + + when { + process { + """ + input[0] = [ + [id:'test'], + [] + ] + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out)).match() } + ) + } + } } diff --git a/modules/nf-core/propr/logratio/tests/main.nf.test.snap b/modules/nf-core/propr/logratio/tests/main.nf.test.snap index a82c427921f4..657fb3099608 100644 --- a/modules/nf-core/propr/logratio/tests/main.nf.test.snap +++ b/modules/nf-core/propr/logratio/tests/main.nf.test.snap @@ -13,11 +13,31 @@ } } ], + "timestamp": "2025-05-16T15:13:57.762737802", "meta": { "nf-test": "0.9.2", "nextflow": "24.10.4" - }, - "timestamp": "2025-05-16T15:13:57.762737802" + } + }, + "mus_musculus - tsv - stub": { + "content": [ + { + "logratio": [ + + ], + "session_info": [ + + ], + "versions": [ + + ] + } + ], + "timestamp": "2026-07-15T10:21:55.800115714", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } }, "mus_musculus - tsv": { "content": [ @@ -40,11 +60,11 @@ } } ], + "timestamp": "2025-05-16T14:35:35.018714127", "meta": { "nf-test": "0.9.2", "nextflow": "24.10.4" - }, - "timestamp": "2025-05-16T14:35:35.018714127" + } }, "mus_musculus - tsv - alr": { "content": [ @@ -67,11 +87,11 @@ } } ], + "timestamp": "2025-05-16T14:42:35.397794344", "meta": { "nf-test": "0.9.2", "nextflow": "24.10.4" - }, - "timestamp": "2025-05-16T14:42:35.397794344" + } }, "mus_musculus - tsv - alr boxcox": { "content": [ @@ -94,11 +114,11 @@ } } ], + "timestamp": "2025-05-16T14:42:43.698056253", "meta": { "nf-test": "0.9.2", "nextflow": "24.10.4" - }, - "timestamp": "2025-05-16T14:42:43.698056253" + } }, "mus_musculus - tsv -- stub": { "content": [ @@ -149,11 +169,11 @@ } } ], + "timestamp": "2025-05-16T14:37:59.786809211", "meta": { "nf-test": "0.9.2", "nextflow": "24.10.4" - }, - "timestamp": "2025-05-16T14:37:59.786809211" + } }, "mus_musculus - tsv - boxcox": { "content": [ @@ -176,11 +196,11 @@ } } ], + "timestamp": "2025-05-16T14:42:28.01694316", "meta": { "nf-test": "0.9.2", "nextflow": "24.10.4" - }, - "timestamp": "2025-05-16T14:42:28.01694316" + } }, "mus_musculus - tsv - alr geneid": { "content": [ @@ -203,11 +223,11 @@ } } ], + "timestamp": "2025-05-16T14:42:51.186760616", "meta": { "nf-test": "0.9.2", "nextflow": "24.10.4" - }, - "timestamp": "2025-05-16T14:42:51.186760616" + } }, "mus_musculus - tsv - alr genename": { "content": [ @@ -230,10 +250,10 @@ } } ], + "timestamp": "2025-05-16T14:42:58.184822937", "meta": { "nf-test": "0.9.2", "nextflow": "24.10.4" - }, - "timestamp": "2025-05-16T14:42:58.184822937" + } } } \ No newline at end of file diff --git a/modules/nf-core/propr/propd/main.nf b/modules/nf-core/propr/propd/main.nf index 21d0616ad3b0..4d5db327d7ac 100644 --- a/modules/nf-core/propr/propd/main.nf +++ b/modules/nf-core/propr/propd/main.nf @@ -27,4 +27,22 @@ process PROPR_PROPD { script: template 'propd.R' + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.propd.genewise.tsv + touch ${prefix}.propd.genewise.png + touch ${prefix}.propd.rds + touch ${prefix}.propd.pairwise.tsv + touch ${prefix}.propd.pairwise_filtered.tsv + touch ${prefix}.propd.adjacency.csv + touch ${prefix}.propd.fdr.tsv + touch ${prefix}.R_sessionInfo.log + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + r-propr: \$(Rscript -e "cat(as.character(packageVersion('propr')))") + END_VERSIONS + """ } diff --git a/modules/nf-core/propr/propd/meta.yml b/modules/nf-core/propr/propd/meta.yml index c2de530d12a7..17fec1ffce9f 100644 --- a/modules/nf-core/propr/propd/meta.yml +++ b/modules/nf-core/propr/propd/meta.yml @@ -65,7 +65,7 @@ output: information as compiled from the propd results pattern: "*.propd.genewise.tsv" ontologies: - - edam: http://edamontology.org/format_3475 + - edam: http://edamontology.org/format_3475 # TSV - "*.propd.genewise.tsv": type: file description: | @@ -73,7 +73,7 @@ output: information as compiled from the propd results pattern: "*.propd.genewise.tsv" ontologies: - - edam: http://edamontology.org/format_3475 + - edam: http://edamontology.org/format_3475 # TSV genewise_plot: - - meta: type: file @@ -82,7 +82,7 @@ output: information as compiled from the propd results pattern: "*.propd.genewise.tsv" ontologies: - - edam: http://edamontology.org/format_3475 + - edam: http://edamontology.org/format_3475 # TSV - "*.propd.genewise.png": type: file description: | @@ -99,7 +99,7 @@ output: information as compiled from the propd results pattern: "*.propd.genewise.tsv" ontologies: - - edam: http://edamontology.org/format_3475 + - edam: http://edamontology.org/format_3475 # TSV - "*.propd.rds": type: file description: | @@ -114,7 +114,7 @@ output: information as compiled from the propd results pattern: "*.propd.genewise.tsv" ontologies: - - edam: http://edamontology.org/format_3475 + - edam: http://edamontology.org/format_3475 # TSV - "*.propd.pairwise.tsv": type: file description: | @@ -123,7 +123,7 @@ output: each pair of genes. pattern: "*.propd.pairwise.tsv" ontologies: - - edam: http://edamontology.org/format_3475 + - edam: http://edamontology.org/format_3475 # TSV results_pairwise_filtered: - - meta: type: file @@ -132,7 +132,7 @@ output: information as compiled from the propd results pattern: "*.propd.genewise.tsv" ontologies: - - edam: http://edamontology.org/format_3475 + - edam: http://edamontology.org/format_3475 # TSV - "*.propd.pairwise_filtered.tsv": type: file description: | @@ -141,7 +141,7 @@ output: proportionality values. pattern: "*.propd.pairwise_filtered.tsv" ontologies: - - edam: http://edamontology.org/format_3475 + - edam: http://edamontology.org/format_3475 # TSV adjacency: - - meta: type: file @@ -150,7 +150,7 @@ output: information as compiled from the propd results pattern: "*.propd.genewise.tsv" ontologies: - - edam: http://edamontology.org/format_3475 + - edam: http://edamontology.org/format_3475 # TSV - "*.propd.adjacency.csv": type: file description: | @@ -159,7 +159,7 @@ output: proportional. pattern: "*.propd.adjacency.csv" ontologies: - - edam: http://edamontology.org/format_3752 + - edam: http://edamontology.org/format_3752 # CSV fdr: - - meta: type: file @@ -168,7 +168,7 @@ output: information as compiled from the propd results pattern: "*.propd.genewise.tsv" ontologies: - - edam: http://edamontology.org/format_3475 + - edam: http://edamontology.org/format_3475 # TSV - "*.propd.fdr.tsv": type: file description: | @@ -178,7 +178,7 @@ output: computationally expensive. pattern: "*.propd.fdr.tsv" ontologies: - - edam: http://edamontology.org/format_3475 + - edam: http://edamontology.org/format_3475 # TSV session_info: - "*.R_sessionInfo.log": type: file @@ -191,7 +191,7 @@ output: description: File containing software versions pattern: "versions.yml" ontologies: - - edam: http://edamontology.org/format_3750 + - edam: http://edamontology.org/format_3750 # YAML topics: versions: - versions.yml: diff --git a/modules/nf-core/propr/propd/tests/main.nf.test b/modules/nf-core/propr/propd/tests/main.nf.test index eae00e1b3663..2b6097921bcb 100755 --- a/modules/nf-core/propr/propd/tests/main.nf.test +++ b/modules/nf-core/propr/propd/tests/main.nf.test @@ -173,4 +173,23 @@ nextflow_process { ) } } + + test("Test propr/propd - stub") { + options "-stub" + + when { + process { + """ + input[0] = [[:], '', '', ''] + input[1] = [[id: 'test'], [], []] + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out)).match() } + ) + } + } } diff --git a/modules/nf-core/propr/propd/tests/main.nf.test.snap b/modules/nf-core/propr/propd/tests/main.nf.test.snap index bb3f18909278..ac7020bcf2c0 100644 --- a/modules/nf-core/propr/propd/tests/main.nf.test.snap +++ b/modules/nf-core/propr/propd/tests/main.nf.test.snap @@ -136,5 +136,78 @@ "nf-test": "0.9.5", "nextflow": "26.04.1" } + }, + "Test propr/propd - stub": { + "content": [ + { + "adjacency": [ + [ + { + + }, + "null.propd.adjacency.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "fdr": [ + [ + { + + }, + "null.propd.fdr.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "genewise_plot": [ + [ + { + + }, + "null.propd.genewise.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "rdata": [ + [ + { + + }, + "null.propd.rds:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "results_genewise": [ + [ + { + + }, + "null.propd.genewise.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "results_pairwise": [ + [ + { + + }, + "null.propd.pairwise.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "results_pairwise_filtered": [ + [ + { + + }, + "null.propd.pairwise_filtered.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "session_info": [ + "null.R_sessionInfo.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "versions": [ + "versions.yml:md5,a6e655144d7d1d743781538442685666" + ] + } + ], + "timestamp": "2026-07-15T10:17:25.950918852", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } } } \ No newline at end of file diff --git a/modules/nf-core/propr/propr/main.nf b/modules/nf-core/propr/propr/main.nf index 8cb37d67da72..21218839446b 100644 --- a/modules/nf-core/propr/propr/main.nf +++ b/modules/nf-core/propr/propr/main.nf @@ -17,11 +17,27 @@ process PROPR_PROPR { tuple val(meta), path("*.adj.csv"), emit: adj , optional:true path "*.warnings.log", emit: warnings path "*.R_sessionInfo.log", emit: session_info - path "versions.yml", emit: versions + path "versions.yml", emit: versions, topic: versions when: task.ext.when == null || task.ext.when script: template 'propr.R' + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.propr.rds + touch ${prefix}.propr.tsv + touch ${prefix}.fdr.tsv + touch ${prefix}.adj.csv + touch ${prefix}.warnings.log + touch ${prefix}.R_sessionInfo.log + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + r-propr: \$(Rscript -e "cat(as.character(packageVersion('propr')))") + END_VERSIONS + """ } diff --git a/modules/nf-core/propr/propr/meta.yml b/modules/nf-core/propr/propr/meta.yml index 20de017cc69b..108668c21718 100644 --- a/modules/nf-core/propr/propr/meta.yml +++ b/modules/nf-core/propr/propr/meta.yml @@ -9,7 +9,6 @@ keywords: - logratio - propr - corpcor - tools: - "propr": description: "Logratio methods for omics data" @@ -17,14 +16,16 @@ tools: documentation: "https://rdrr.io/cran/propr/man/propr.html" tool_dev_url: "https://github.com/tpq/propr" doi: "10.1038/s41598-017-16520-0" - licence: ["GPL-2"] + licence: + - "GPL-2" identifier: biotools:propr - "corpcor": description: "Efficient Estimation of Covariance and (Partial) Correlation" homepage: "https://cran.r-project.org/web/packages/corpcor/index.html" documentation: "https://cran.r-project.org/web/packages/corpcor/corpcor.pdf" doi: "10.2202/1544-6115.1175" - licence: ["GPL >=3"] + licence: + - "GPL >=3" identifier: biotools:propr input: @@ -115,5 +116,10 @@ output: pattern: "versions.yml" ontologies: - edam: http://edamontology.org/format_3750 # YAML +topics: + versions: + - versions.yml: + type: string + description: The name of the process authors: - "@suzannejin" diff --git a/modules/nf-core/propr/propr/tests/main.nf.test b/modules/nf-core/propr/propr/tests/main.nf.test index f2e371e80bf1..cc0ec438f436 100644 --- a/modules/nf-core/propr/propr/tests/main.nf.test +++ b/modules/nf-core/propr/propr/tests/main.nf.test @@ -237,4 +237,25 @@ nextflow_process { ) } } + + test("Test propr/propr - stub") { + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], + [] + ] + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out)).match() } + ) + } + } } diff --git a/modules/nf-core/propr/propr/tests/main.nf.test.snap b/modules/nf-core/propr/propr/tests/main.nf.test.snap index cde969bc16f5..468e4f5ff52f 100644 --- a/modules/nf-core/propr/propr/tests/main.nf.test.snap +++ b/modules/nf-core/propr/propr/tests/main.nf.test.snap @@ -10,11 +10,11 @@ ] ] ], + "timestamp": "2024-04-05T11:22:00.577754", "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" - }, - "timestamp": "2024-04-05T11:22:00.577754" + } }, "Test propr/propr calculating adjacency_matrix for rho - fdr": { "content": [ @@ -27,11 +27,11 @@ ] ] ], + "timestamp": "2024-04-05T11:23:04.464473", "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" - }, - "timestamp": "2024-04-05T11:23:04.464473" + } }, "Test propr/propr calculating adjacency_matrix for pcor - adj": { "content": [ @@ -44,11 +44,11 @@ ] ] ], + "timestamp": "2024-04-05T11:24:45.008049", "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" - }, - "timestamp": "2024-04-05T11:24:45.008049" + } }, "Test propr/propr while running alr+pcor.bshrink - fdr": { "content": [ @@ -61,11 +61,11 @@ ] ] ], + "timestamp": "2024-04-05T11:20:50.487477", "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" - }, - "timestamp": "2024-04-05T11:20:50.487477" + } }, "Test propr/propr using default options - matrix": { "content": [ @@ -78,11 +78,11 @@ ] ] ], + "timestamp": "2024-04-05T11:19:27.698729", "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" - }, - "timestamp": "2024-04-05T11:19:27.698729" + } }, "Test propr/propr calculating adjacency_matrix for phs - adj": { "content": [ @@ -95,11 +95,11 @@ ] ] ], + "timestamp": "2024-04-05T11:23:45.966557", "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" - }, - "timestamp": "2024-04-05T11:23:45.966557" + } }, "Test propr/propr while running clr+pcor.bshrink explicitly - matrix": { "content": [ @@ -112,11 +112,11 @@ ] ] ], + "timestamp": "2024-04-05T11:20:07.836881", "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" - }, - "timestamp": "2024-04-05T11:20:07.836881" + } }, "Test propr/propr while running clr+pcor - matrix": { "content": [ @@ -129,11 +129,11 @@ ] ] ], + "timestamp": "2024-04-05T11:21:59.693747", "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" - }, - "timestamp": "2024-04-05T11:21:59.693747" + } }, "Test propr/propr while running alr+pcor.bshrink - matrix": { "content": [ @@ -146,11 +146,11 @@ ] ] ], + "timestamp": "2024-04-05T11:20:49.898429", "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" - }, - "timestamp": "2024-04-05T11:20:49.898429" + } }, "Test propr/propr calculating adjacency_matrix for pcor - fdr": { "content": [ @@ -163,11 +163,63 @@ ] ] ], + "timestamp": "2024-04-05T11:24:43.724784", "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" - }, - "timestamp": "2024-04-05T11:24:43.724784" + } + }, + "Test propr/propr - stub": { + "content": [ + { + "adj": [ + [ + { + "id": "test" + }, + "test.adj.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "fdr": [ + [ + { + "id": "test" + }, + "test.fdr.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "matrix": [ + [ + { + "id": "test" + }, + "test.propr.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "propr": [ + [ + { + "id": "test" + }, + "test.propr.rds:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "session_info": [ + "test.R_sessionInfo.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "versions": [ + "versions.yml:md5,2e3159924c190ab42e22a4d0e192b1e6" + ], + "warnings": [ + "test.warnings.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + } + ], + "timestamp": "2026-07-15T10:20:50.181642955", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } }, "Test propr/propr while running clr+rho - fdr": { "content": [ @@ -180,11 +232,11 @@ ] ] ], + "timestamp": "2024-04-05T11:21:19.887004", "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" - }, - "timestamp": "2024-04-05T11:21:19.887004" + } }, "Test propr/propr while running clr+rho - matrix": { "content": [ @@ -197,11 +249,11 @@ ] ] ], + "timestamp": "2024-04-05T11:21:19.194321", "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" - }, - "timestamp": "2024-04-05T11:21:19.194321" + } }, "versions": { "content": [ @@ -209,11 +261,11 @@ "versions.yml:md5,2e3159924c190ab42e22a4d0e192b1e6" ] ], + "timestamp": "2024-04-05T11:19:27.963267", "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" - }, - "timestamp": "2024-04-05T11:19:27.963267" + } }, "Test propr/propr calculating adjacency_matrix for phs - fdr": { "content": [ @@ -226,11 +278,11 @@ ] ] ], + "timestamp": "2024-04-05T11:23:44.841504", "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" - }, - "timestamp": "2024-04-05T11:23:44.841504" + } }, "Test propr/propr calculating adjacency_matrix for pcor - matrix": { "content": [ @@ -243,11 +295,11 @@ ] ] ], + "timestamp": "2024-04-05T11:24:41.975415", "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" - }, - "timestamp": "2024-04-05T11:24:41.975415" + } }, "Test propr/propr while running clr+rho with boxcox transformation - fdr": { "content": [ @@ -260,11 +312,11 @@ ] ] ], + "timestamp": "2024-04-05T11:22:29.830787", "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" - }, - "timestamp": "2024-04-05T11:22:29.830787" + } }, "Test propr/propr calculating adjacency_matrix for rho - adj": { "content": [ @@ -277,11 +329,11 @@ ] ] ], + "timestamp": "2024-04-05T11:23:05.438967", "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" - }, - "timestamp": "2024-04-05T11:23:05.438967" + } }, "Test propr/propr while running clr+rho with boxcox transformation - matrix": { "content": [ @@ -294,11 +346,11 @@ ] ] ], + "timestamp": "2024-04-05T11:22:28.793097", "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" - }, - "timestamp": "2024-04-05T11:22:28.793097" + } }, "Test propr/propr calculating adjacency_matrix for rho - matrix": { "content": [ @@ -311,11 +363,11 @@ ] ] ], + "timestamp": "2024-04-05T11:23:03.240604", "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" - }, - "timestamp": "2024-04-05T11:23:03.240604" + } }, "Test propr/propr while running clr+pcor.bshrink explicitly - fdr": { "content": [ @@ -328,11 +380,11 @@ ] ] ], + "timestamp": "2024-04-05T11:20:08.230977", "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" - }, - "timestamp": "2024-04-05T11:20:08.230977" + } }, "Test propr/propr calculating adjacency_matrix for phs - matrix": { "content": [ @@ -345,10 +397,10 @@ ] ] ], + "timestamp": "2024-04-05T11:23:43.441629", "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" - }, - "timestamp": "2024-04-05T11:23:43.441629" + } } } \ No newline at end of file From 32bbf178df41eb7fd4018f783695d30543f5a884 Mon Sep 17 00:00:00 2001 From: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Date: Mon, 20 Jul 2026 10:05:28 +0000 Subject: [PATCH 8/9] Swap propr to topics --- .../tests/main.nf.test.snap | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test.snap b/subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test.snap index fdd87d2089aa..6b61d04bab08 100644 --- a/subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test.snap +++ b/subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test.snap @@ -59,7 +59,7 @@ "differential_method": "propd", "functional_method": "grea" }, - "treatment_mCherry_hND6__test.grea.tsv:md5,bf4e67ff65904bd8885b3f4df94d447f" + "treatment_mCherry_hND6__test.grea.tsv:md5,1774613033c208d2e35f3aadd6ff95ad" ], [ { @@ -71,11 +71,11 @@ "differential_method": "propd", "functional_method": "grea" }, - "treatment_mCherry_hND6_sample_number_test.grea.tsv:md5,d78b2e198a17432132a2c77ede56348f" + "treatment_mCherry_hND6_sample_number_test.grea.tsv:md5,a781c46db63ef350f2ccc403cb570d8e" ] ] ], - "timestamp": "2026-07-15T09:45:04.500465719", + "timestamp": "2026-07-17T06:18:28.731481848", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.6" @@ -178,7 +178,7 @@ "differential_method": "propd", "functional_method": "grea" }, - "treatment_mCherry_hND6__test.grea.tsv:md5,5dab18c7b33d1b1f89e7a0fff1ef2e22" + "treatment_mCherry_hND6__test.grea.tsv:md5,59c013c4109e65b81ec872286ccfaedc" ], [ { @@ -190,11 +190,11 @@ "differential_method": "propd", "functional_method": "grea" }, - "treatment_mCherry_hND6_sample_number_test.grea.tsv:md5,03919cdb3800f126cb39127d169b7a6f" + "treatment_mCherry_hND6_sample_number_test.grea.tsv:md5,f95b4f4c58f4f3c2cc11db699d776eab" ] ] ], - "timestamp": "2026-07-15T09:44:02.650524377", + "timestamp": "2026-07-17T06:17:38.011066593", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.6" From 0d397b45c6f2a007681888ee3d725f7e0d72dc03 Mon Sep 17 00:00:00 2001 From: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Date: Mon, 27 Jul 2026 17:14:03 +0000 Subject: [PATCH 9/9] Update assertions --- modules/nf-core/propr/grea/tests/main.nf.test | 2 +- .../nf-core/propr/logratio/tests/main.nf.test | 26 +- .../propr/logratio/tests/main.nf.test.snap | 121 +- .../tests/main.nf.test | 6 +- .../tests/main.nf.test.snap | 1380 ++++++++++++++++- 5 files changed, 1358 insertions(+), 177 deletions(-) diff --git a/modules/nf-core/propr/grea/tests/main.nf.test b/modules/nf-core/propr/grea/tests/main.nf.test index 7b0f35adc4ec..875f4a216671 100644 --- a/modules/nf-core/propr/grea/tests/main.nf.test +++ b/modules/nf-core/propr/grea/tests/main.nf.test @@ -56,7 +56,7 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - sanitizeOutput(process.out), + sanitizeOutput(process.out, unstableKeys: ["session_info"]), path(process.out.versions[0]).yaml ).match() } ) diff --git a/modules/nf-core/propr/logratio/tests/main.nf.test b/modules/nf-core/propr/logratio/tests/main.nf.test index 44621e30cf5f..670542838fa1 100644 --- a/modules/nf-core/propr/logratio/tests/main.nf.test +++ b/modules/nf-core/propr/logratio/tests/main.nf.test @@ -199,8 +199,7 @@ nextflow_process { ) } } - test("mus_musculus - tsv -- stub") { - tag "stub" + test("mus_musculus - tsv - stub") { options "-stub" when { params { @@ -220,31 +219,10 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - process.out, + sanitizeOutput(process.out), path(process.out.versions[0]).yaml ).match() } ) } } - - test("mus_musculus - tsv - stub") { - options "-stub" - - when { - process { - """ - input[0] = [ - [id:'test'], - [] - ] - """ - } - } - then { - assertAll( - { assert process.success }, - { assert snapshot(sanitizeOutput(process.out)).match() } - ) - } - } } diff --git a/modules/nf-core/propr/logratio/tests/main.nf.test.snap b/modules/nf-core/propr/logratio/tests/main.nf.test.snap index 657fb3099608..ddd7c532b690 100644 --- a/modules/nf-core/propr/logratio/tests/main.nf.test.snap +++ b/modules/nf-core/propr/logratio/tests/main.nf.test.snap @@ -13,27 +13,43 @@ } } ], - "timestamp": "2025-05-16T15:13:57.762737802", + "timestamp": "2026-07-20T10:32:31.426923165", "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nf-test": "0.9.5", + "nextflow": "26.04.6" } }, "mus_musculus - tsv - stub": { "content": [ { "logratio": [ - + [ + { + "id": "test" + }, + "test.clr.NA.NA.logratio.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "session_info": [ - + [ + { + "id": "test" + }, + "test.clr.NA.NA.R_sessionInfo.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "versions": [ - + "versions.yml:md5,17854c506bb1d60e003349d189b206b9" ] + }, + { + "PROPR_LOGRATIO": { + "r-base": "4.3.0", + "r-propr": "4.2.6" + } } ], - "timestamp": "2026-07-15T10:21:55.800115714", + "timestamp": "2026-07-20T10:32:37.010585304", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.6" @@ -60,10 +76,10 @@ } } ], - "timestamp": "2025-05-16T14:35:35.018714127", + "timestamp": "2026-07-20T10:31:58.297049568", "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nf-test": "0.9.5", + "nextflow": "26.04.6" } }, "mus_musculus - tsv - alr": { @@ -87,10 +103,10 @@ } } ], - "timestamp": "2025-05-16T14:42:35.397794344", + "timestamp": "2026-07-20T10:32:09.35463478", "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nf-test": "0.9.5", + "nextflow": "26.04.6" } }, "mus_musculus - tsv - alr boxcox": { @@ -114,65 +130,10 @@ } } ], - "timestamp": "2025-05-16T14:42:43.698056253", + "timestamp": "2026-07-20T10:32:14.799953464", "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.4" - } - }, - "mus_musculus - tsv -- stub": { - "content": [ - { - "0": [ - [ - { - "id": "test" - }, - "test.clr.NA.NA.logratio.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test" - }, - "test.clr.NA.NA.R_sessionInfo.log:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - "versions.yml:md5,17854c506bb1d60e003349d189b206b9" - ], - "logratio": [ - [ - { - "id": "test" - }, - "test.clr.NA.NA.logratio.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "session_info": [ - [ - { - "id": "test" - }, - "test.clr.NA.NA.R_sessionInfo.log:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,17854c506bb1d60e003349d189b206b9" - ] - }, - { - "PROPR_LOGRATIO": { - "r-base": "4.3.0", - "r-propr": "4.2.6" - } - } - ], - "timestamp": "2025-05-16T14:37:59.786809211", - "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nf-test": "0.9.5", + "nextflow": "26.04.6" } }, "mus_musculus - tsv - boxcox": { @@ -196,10 +157,10 @@ } } ], - "timestamp": "2025-05-16T14:42:28.01694316", + "timestamp": "2026-07-20T10:32:03.694465188", "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nf-test": "0.9.5", + "nextflow": "26.04.6" } }, "mus_musculus - tsv - alr geneid": { @@ -223,10 +184,10 @@ } } ], - "timestamp": "2025-05-16T14:42:51.186760616", + "timestamp": "2026-07-20T10:32:20.46939457", "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nf-test": "0.9.5", + "nextflow": "26.04.6" } }, "mus_musculus - tsv - alr genename": { @@ -250,10 +211,10 @@ } } ], - "timestamp": "2025-05-16T14:42:58.184822937", + "timestamp": "2026-07-20T10:32:25.997962278", "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nf-test": "0.9.5", + "nextflow": "26.04.6" } } } \ No newline at end of file diff --git a/subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test b/subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test index a4f0db79cfba..f93d72202c62 100644 --- a/subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test +++ b/subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test @@ -474,11 +474,7 @@ nextflow_workflow { assertAll( { assert workflow.success}, { assert snapshot( - path(workflow.out.gprofiler2_all_enrich[0][1]).exists(), // This generates empty md5sums and linting fails - workflow.out.gprofiler2_sub_enrich, - workflow.out.gprofiler2_plot_html.collect{ meta, html -> file(html).name }, //assert unstable file - workflow.out.gsea_report, - workflow.out.grea_results + sanitizeOutput(workflow.out, unstableKeys: ["gprofiler2_all_enrich", "gprofiler2_plot_html", "grea_results", "session_info", "rpt"]) ).match()}, ) } diff --git a/subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test.snap b/subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test.snap index 6b61d04bab08..d62870619968 100644 --- a/subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test.snap +++ 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