From 9e506ed932457726fa9acc7ac1a917f4ac100276 Mon Sep 17 00:00:00 2001 From: manascripts Date: Wed, 15 Jul 2026 15:12:29 +0200 Subject: [PATCH 1/7] add new module: octopusv/plotcircos --- .../octopusv/plotcircos/environment.yml | 7 ++ modules/nf-core/octopusv/plotcircos/main.nf | 45 +++++++++ modules/nf-core/octopusv/plotcircos/meta.yml | 93 +++++++++++++++++++ .../octopusv/plotcircos/tests/main.nf.test | 62 +++++++++++++ .../plotcircos/tests/main.nf.test.snap | 55 +++++++++++ 5 files changed, 262 insertions(+) create mode 100644 modules/nf-core/octopusv/plotcircos/environment.yml create mode 100644 modules/nf-core/octopusv/plotcircos/main.nf create mode 100644 modules/nf-core/octopusv/plotcircos/meta.yml create mode 100644 modules/nf-core/octopusv/plotcircos/tests/main.nf.test create mode 100644 modules/nf-core/octopusv/plotcircos/tests/main.nf.test.snap diff --git a/modules/nf-core/octopusv/plotcircos/environment.yml b/modules/nf-core/octopusv/plotcircos/environment.yml new file mode 100644 index 000000000000..7a8fad1655d6 --- /dev/null +++ b/modules/nf-core/octopusv/plotcircos/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - "bioconda::octopusv=0.4.0" diff --git a/modules/nf-core/octopusv/plotcircos/main.nf b/modules/nf-core/octopusv/plotcircos/main.nf new file mode 100644 index 000000000000..1a03acf50550 --- /dev/null +++ b/modules/nf-core/octopusv/plotcircos/main.nf @@ -0,0 +1,45 @@ +process OCTOPUSV_PLOTCIRCOS { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/octopusv:0.4.0--pyhdfd78af_0': + 'quay.io/biocontainers/octopusv:0.4.0--pyhdfd78af_0' }" + + input: + tuple val(meta), path(svcf), val(output_format) + path(fai) + + output: + tuple val(meta), path("${prefix}.circos.${output_format}"), emit: circos + tuple val(meta), path("${prefix}.circos.oversized_intra.tsv"), emit: oversized_intra + tuple val("${task.process}"), val('octopusv'), eval("python -c \"import importlib.metadata as m; print(m.version('octopusv'))\""), emit: versions_octopusv, topic: versions + + script: + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + def fai_arg = fai ? "--fai ${fai}" : "" + def supported_formats = ['pdf', 'png', 'svg'] + + if (!(output_format in supported_formats)) { + error "Unsupported Circos output format: ${output_format}. Supported formats: ${supported_formats.join(', ')}" + } + + """ + octopusv plot-circos \\ + --input-file ${svcf} \\ + --output-file ${prefix}.circos.${output_format} \\ + --sample ${prefix} \\ + ${fai_arg} \\ + ${args} + """ + + stub: + prefix = task.ext.prefix ?: "${meta.id}" + + """ + touch ${prefix}.circos.${output_format} + touch ${prefix}.circos.oversized_intra.tsv + """ +} diff --git a/modules/nf-core/octopusv/plotcircos/meta.yml b/modules/nf-core/octopusv/plotcircos/meta.yml new file mode 100644 index 000000000000..0f6da43b1478 --- /dev/null +++ b/modules/nf-core/octopusv/plotcircos/meta.yml @@ -0,0 +1,93 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "octopusv_plotcircos" +description: "Draw a genome-wide structural variant Circos plot from an OctopuSV SVCF file." +keywords: + - structural variant + - circos + - plot + - visualisation +tools: + - "octopusv": + description: "End-to-end structural variant post-processing: standardize, merge, + compare, and export SVs." + homepage: "https://github.com/ylab-hi/OctopuSV" + documentation: "https://github.com/ylab-hi/OctopuSV" + tool_dev_url: "https://github.com/ylab-hi/octopusV" + doi: "10.1093/bioinformatics/btaf599" + licence: + - "MIT" + identifier: "" + +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - svcf: + type: file + description: Structural variant call file in OctopuSV SVCF format + pattern: "*.svcf" + ontologies: + - edam: "http://edamontology.org/format_3016" # VCF + - fai: + type: file + description: Optional reference FASTA index used to define chromosome sizes; built-in hg38 sizes are used when absent + pattern: "*.fai" + optional: true + ontologies: + - edam: "http://edamontology.org/format_3475" # TSV +output: + circos: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "${prefix}.circos.${output_format}": + type: file + description: Genome-wide structural variant Circos plot in the requested output format + pattern: "*circos.${output_format}" + ontologies: + - edam: "http://edamontology.org/format_3508" # PDF + - edam: "http://edamontology.org/format_3603" # PNG + - edam: "http://edamontology.org/format_3604" # SVG + oversized_intra: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - ${prefix}.circos.oversized_intra.tsv: + type: file + description: Intra-chromosomal structural variants exceeding the maximum displayed span + pattern: "*.circos.oversized_intra.tsv" + ontologies: + - edam: "http://edamontology.org/format_3475" # TSV + versions_octopusv: + - - ${task.process}: + type: string + description: The name of the process + - octopusv: + type: string + description: The name of the tool + - python -c "import importlib.metadata as m; print(m.version('octopusv'))": + type: eval + description: The expression to obtain the version of the tool + +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - octopusv: + type: string + description: The name of the tool + - python -c "import importlib.metadata as m; print(m.version('octopusv'))": + type: eval + description: The expression to obtain the version of the tool + +authors: + - "@manascripts" +maintainers: + - "@manascripts" diff --git a/modules/nf-core/octopusv/plotcircos/tests/main.nf.test b/modules/nf-core/octopusv/plotcircos/tests/main.nf.test new file mode 100644 index 000000000000..a9905e725b26 --- /dev/null +++ b/modules/nf-core/octopusv/plotcircos/tests/main.nf.test @@ -0,0 +1,62 @@ +nextflow_process { + + name "Test Process OCTOPUSV_PLOTCIRCOS" + script "../main.nf" + process "OCTOPUSV_PLOTCIRCOS" + + tag "modules" + tag "modules_nfcore" + tag "octopusv" + tag "octopusv/plotcircos" + + test("homo_sapiens - svcf") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/octopusv/sk-n-as-severus-ont.svcf', checkIfExists: true), + 'pdf' + ] + input[1] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.circos.get(0).get(1)), + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() } + ) + } + } + + test("homo_sapiens - svcf - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/octopusv/sk-n-as-severus-ont.svcf', checkIfExists: true), + 'pdf' + ] + input[1] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out)).match() } + ) + } + } +} diff --git a/modules/nf-core/octopusv/plotcircos/tests/main.nf.test.snap b/modules/nf-core/octopusv/plotcircos/tests/main.nf.test.snap new file mode 100644 index 000000000000..301117e3574c --- /dev/null +++ b/modules/nf-core/octopusv/plotcircos/tests/main.nf.test.snap @@ -0,0 +1,55 @@ +{ + "homo_sapiens - svcf": { + "content": [ + "test.circos.pdf:md5,ed51f3869a483296cc29ac1f659f27e0", + { + "versions_octopusv": [ + [ + "OCTOPUSV_PLOTCIRCOS", + "octopusv", + "0.4.0" + ] + ] + } + ], + "timestamp": "2026-07-15T12:44:17.320334956", + "meta": { + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } + }, + "homo_sapiens - svcf - stub": { + "content": [ + { + "circos": [ + [ + { + "id": "test" + }, + "test.circos.pdf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "oversized_intra": [ + [ + { + "id": "test" + }, + "test.circos.oversized_intra.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_octopusv": [ + [ + "OCTOPUSV_PLOTCIRCOS", + "octopusv", + "0.4.0" + ] + ] + } + ], + "timestamp": "2026-07-15T12:44:25.747576759", + "meta": { + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } + } +} \ No newline at end of file From 135075b10a758cb494866214136b76cf15b68054 Mon Sep 17 00:00:00 2001 From: manascripts Date: Wed, 15 Jul 2026 15:50:25 +0200 Subject: [PATCH 2/7] meta.yml update --- modules/nf-core/octopusv/plotcircos/main.nf | 3 +++ modules/nf-core/octopusv/plotcircos/meta.yml | 3 +++ 2 files changed, 6 insertions(+) diff --git a/modules/nf-core/octopusv/plotcircos/main.nf b/modules/nf-core/octopusv/plotcircos/main.nf index 1a03acf50550..51791dda7566 100644 --- a/modules/nf-core/octopusv/plotcircos/main.nf +++ b/modules/nf-core/octopusv/plotcircos/main.nf @@ -16,6 +16,9 @@ process OCTOPUSV_PLOTCIRCOS { tuple val(meta), path("${prefix}.circos.oversized_intra.tsv"), emit: oversized_intra tuple val("${task.process}"), val('octopusv'), eval("python -c \"import importlib.metadata as m; print(m.version('octopusv'))\""), emit: versions_octopusv, topic: versions + when: + task.ext.when == null || task.ext.when + script: def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}" diff --git a/modules/nf-core/octopusv/plotcircos/meta.yml b/modules/nf-core/octopusv/plotcircos/meta.yml index 0f6da43b1478..7f6edc670518 100644 --- a/modules/nf-core/octopusv/plotcircos/meta.yml +++ b/modules/nf-core/octopusv/plotcircos/meta.yml @@ -30,6 +30,9 @@ input: pattern: "*.svcf" ontologies: - edam: "http://edamontology.org/format_3016" # VCF + - output_format: + type: string + description: Output format for the Circos plot (valid values - pdf, png, svg) - fai: type: file description: Optional reference FASTA index used to define chromosome sizes; built-in hg38 sizes are used when absent From e953e4c72cf927ef42afd5dd49d95e45f1bfe338 Mon Sep 17 00:00:00 2001 From: Manas Date: Wed, 15 Jul 2026 15:57:41 +0200 Subject: [PATCH 3/7] Update modules/nf-core/octopusv/plotcircos/main.nf MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- modules/nf-core/octopusv/plotcircos/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/octopusv/plotcircos/main.nf b/modules/nf-core/octopusv/plotcircos/main.nf index 51791dda7566..1d607e2c130f 100644 --- a/modules/nf-core/octopusv/plotcircos/main.nf +++ b/modules/nf-core/octopusv/plotcircos/main.nf @@ -14,7 +14,7 @@ process OCTOPUSV_PLOTCIRCOS { output: tuple val(meta), path("${prefix}.circos.${output_format}"), emit: circos tuple val(meta), path("${prefix}.circos.oversized_intra.tsv"), emit: oversized_intra - tuple val("${task.process}"), val('octopusv'), eval("python -c \"import importlib.metadata as m; print(m.version('octopusv'))\""), emit: versions_octopusv, topic: versions + tuple val("${task.process}"), val('octopusv'), eval("octopusv --help | sed -n 's/^ *Version: *//p'"), emit: versions_octopusv, topic: versions when: task.ext.when == null || task.ext.when From 1d76c22429601a37d629e6542138b338d44d75db Mon Sep 17 00:00:00 2001 From: manascripts Date: Thu, 16 Jul 2026 10:04:51 +0200 Subject: [PATCH 4/7] review feedback - update tests --- .../octopusv/plotcircos/tests/main.nf.test | 2 +- .../plotcircos/tests/main.nf.test.snap | 57 +++++++++++++++++-- 2 files changed, 53 insertions(+), 6 deletions(-) diff --git a/modules/nf-core/octopusv/plotcircos/tests/main.nf.test b/modules/nf-core/octopusv/plotcircos/tests/main.nf.test index a9905e725b26..58dbdf549568 100644 --- a/modules/nf-core/octopusv/plotcircos/tests/main.nf.test +++ b/modules/nf-core/octopusv/plotcircos/tests/main.nf.test @@ -28,7 +28,7 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - file(process.out.circos.get(0).get(1)), + process.out, process.out.findAll { key, val -> key.startsWith('versions') } ).match() } ) diff --git a/modules/nf-core/octopusv/plotcircos/tests/main.nf.test.snap b/modules/nf-core/octopusv/plotcircos/tests/main.nf.test.snap index 301117e3574c..86becda4df71 100644 --- a/modules/nf-core/octopusv/plotcircos/tests/main.nf.test.snap +++ b/modules/nf-core/octopusv/plotcircos/tests/main.nf.test.snap @@ -1,18 +1,65 @@ { "homo_sapiens - svcf": { "content": [ - "test.circos.pdf:md5,ed51f3869a483296cc29ac1f659f27e0", + { + "0": [ + [ + { + "id": "test" + }, + "test.circos.pdf:md5,247c352b7a1be9080429392145c4e34a" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.circos.oversized_intra.tsv:md5,bcfe4be36eda15275d2cda3ff1ce7bd0" + ] + ], + "2": [ + [ + "OCTOPUSV_PLOTCIRCOS", + "octopusv", + "0.4.0 " + ] + ], + "circos": [ + [ + { + "id": "test" + }, + "test.circos.pdf:md5,247c352b7a1be9080429392145c4e34a" + ] + ], + "oversized_intra": [ + [ + { + "id": "test" + }, + "test.circos.oversized_intra.tsv:md5,bcfe4be36eda15275d2cda3ff1ce7bd0" + ] + ], + "versions_octopusv": [ + [ + "OCTOPUSV_PLOTCIRCOS", + "octopusv", + "0.4.0 " + ] + ] + }, { "versions_octopusv": [ [ "OCTOPUSV_PLOTCIRCOS", "octopusv", - "0.4.0" + "0.4.0 " ] ] } ], - "timestamp": "2026-07-15T12:44:17.320334956", + "timestamp": "2026-07-15T16:32:47.08911967", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" @@ -41,12 +88,12 @@ [ "OCTOPUSV_PLOTCIRCOS", "octopusv", - "0.4.0" + "0.4.0 " ] ] } ], - "timestamp": "2026-07-15T12:44:25.747576759", + "timestamp": "2026-07-15T16:32:59.302946632", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" From 3244100e5c85834abbf331a0b9e39b3c2b0ad09b Mon Sep 17 00:00:00 2001 From: manascripts Date: Thu, 16 Jul 2026 10:21:33 +0200 Subject: [PATCH 5/7] update snapshot --- modules/nf-core/octopusv/plotcircos/meta.yml | 4 ++-- .../nf-core/octopusv/plotcircos/tests/main.nf.test.snap | 8 ++++---- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/modules/nf-core/octopusv/plotcircos/meta.yml b/modules/nf-core/octopusv/plotcircos/meta.yml index 7f6edc670518..eb5f361bc3f7 100644 --- a/modules/nf-core/octopusv/plotcircos/meta.yml +++ b/modules/nf-core/octopusv/plotcircos/meta.yml @@ -74,7 +74,7 @@ output: - octopusv: type: string description: The name of the tool - - python -c "import importlib.metadata as m; print(m.version('octopusv'))": + - "octopusv --help | sed -n 's/^ *Version: *//p'": type: eval description: The expression to obtain the version of the tool @@ -86,7 +86,7 @@ topics: - octopusv: type: string description: The name of the tool - - python -c "import importlib.metadata as m; print(m.version('octopusv'))": + - "octopusv --help | sed -n 's/^ *Version: *//p'": type: eval description: The expression to obtain the version of the tool diff --git a/modules/nf-core/octopusv/plotcircos/tests/main.nf.test.snap b/modules/nf-core/octopusv/plotcircos/tests/main.nf.test.snap index 86becda4df71..f1db9422424f 100644 --- a/modules/nf-core/octopusv/plotcircos/tests/main.nf.test.snap +++ b/modules/nf-core/octopusv/plotcircos/tests/main.nf.test.snap @@ -7,7 +7,7 @@ { "id": "test" }, - "test.circos.pdf:md5,247c352b7a1be9080429392145c4e34a" + "test.circos.pdf:md5,66efc60e3c2266b8f8cc44dcd9fef1d7" ] ], "1": [ @@ -30,7 +30,7 @@ { "id": "test" }, - "test.circos.pdf:md5,247c352b7a1be9080429392145c4e34a" + "test.circos.pdf:md5,66efc60e3c2266b8f8cc44dcd9fef1d7" ] ], "oversized_intra": [ @@ -59,7 +59,7 @@ ] } ], - "timestamp": "2026-07-15T16:32:47.08911967", + "timestamp": "2026-07-16T10:20:39.441337134", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" @@ -93,7 +93,7 @@ ] } ], - "timestamp": "2026-07-15T16:32:59.302946632", + "timestamp": "2026-07-16T10:20:52.637472113", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" From ec7433c8071502d06df61715e18584b1a21d18f5 Mon Sep 17 00:00:00 2001 From: manascripts Date: Thu, 16 Jul 2026 13:50:57 +0200 Subject: [PATCH 6/7] update tests 2.0 --- modules/nf-core/octopusv/plotcircos/main.nf | 2 +- modules/nf-core/octopusv/plotcircos/meta.yml | 4 +- .../octopusv/plotcircos/tests/main.nf.test | 6 +-- .../plotcircos/tests/main.nf.test.snap | 37 ++++--------------- 4 files changed, 13 insertions(+), 36 deletions(-) diff --git a/modules/nf-core/octopusv/plotcircos/main.nf b/modules/nf-core/octopusv/plotcircos/main.nf index 1d607e2c130f..51791dda7566 100644 --- a/modules/nf-core/octopusv/plotcircos/main.nf +++ b/modules/nf-core/octopusv/plotcircos/main.nf @@ -14,7 +14,7 @@ process OCTOPUSV_PLOTCIRCOS { output: tuple val(meta), path("${prefix}.circos.${output_format}"), emit: circos tuple val(meta), path("${prefix}.circos.oversized_intra.tsv"), emit: oversized_intra - tuple val("${task.process}"), val('octopusv'), eval("octopusv --help | sed -n 's/^ *Version: *//p'"), emit: versions_octopusv, topic: versions + tuple val("${task.process}"), val('octopusv'), eval("python -c \"import importlib.metadata as m; print(m.version('octopusv'))\""), emit: versions_octopusv, topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/octopusv/plotcircos/meta.yml b/modules/nf-core/octopusv/plotcircos/meta.yml index eb5f361bc3f7..7f6edc670518 100644 --- a/modules/nf-core/octopusv/plotcircos/meta.yml +++ b/modules/nf-core/octopusv/plotcircos/meta.yml @@ -74,7 +74,7 @@ output: - octopusv: type: string description: The name of the tool - - "octopusv --help | sed -n 's/^ *Version: *//p'": + - python -c "import importlib.metadata as m; print(m.version('octopusv'))": type: eval description: The expression to obtain the version of the tool @@ -86,7 +86,7 @@ topics: - octopusv: type: string description: The name of the tool - - "octopusv --help | sed -n 's/^ *Version: *//p'": + - python -c "import importlib.metadata as m; print(m.version('octopusv'))": type: eval description: The expression to obtain the version of the tool diff --git a/modules/nf-core/octopusv/plotcircos/tests/main.nf.test b/modules/nf-core/octopusv/plotcircos/tests/main.nf.test index 58dbdf549568..3a0dec6ccc02 100644 --- a/modules/nf-core/octopusv/plotcircos/tests/main.nf.test +++ b/modules/nf-core/octopusv/plotcircos/tests/main.nf.test @@ -17,7 +17,7 @@ nextflow_process { input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/octopusv/sk-n-as-severus-ont.svcf', checkIfExists: true), - 'pdf' + 'png' ] input[1] = [] """ @@ -28,7 +28,7 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - process.out, + sanitizeOutput(process.out), process.out.findAll { key, val -> key.startsWith('versions') } ).match() } ) @@ -45,7 +45,7 @@ nextflow_process { input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/octopusv/sk-n-as-severus-ont.svcf', checkIfExists: true), - 'pdf' + 'png' ] input[1] = [] """ diff --git a/modules/nf-core/octopusv/plotcircos/tests/main.nf.test.snap b/modules/nf-core/octopusv/plotcircos/tests/main.nf.test.snap index f1db9422424f..128240e8f949 100644 --- a/modules/nf-core/octopusv/plotcircos/tests/main.nf.test.snap +++ b/modules/nf-core/octopusv/plotcircos/tests/main.nf.test.snap @@ -2,35 +2,12 @@ "homo_sapiens - svcf": { "content": [ { - "0": [ - [ - { - "id": "test" - }, - "test.circos.pdf:md5,66efc60e3c2266b8f8cc44dcd9fef1d7" - ] - ], - "1": [ - [ - { - "id": "test" - }, - "test.circos.oversized_intra.tsv:md5,bcfe4be36eda15275d2cda3ff1ce7bd0" - ] - ], - "2": [ - [ - "OCTOPUSV_PLOTCIRCOS", - "octopusv", - "0.4.0 " - ] - ], "circos": [ [ { "id": "test" }, - "test.circos.pdf:md5,66efc60e3c2266b8f8cc44dcd9fef1d7" + "test.circos.png:md5,a47ceda3176b0686a5b73fac95b6e30e" ] ], "oversized_intra": [ @@ -45,7 +22,7 @@ [ "OCTOPUSV_PLOTCIRCOS", "octopusv", - "0.4.0 " + "0.4.0" ] ] }, @@ -54,12 +31,12 @@ [ "OCTOPUSV_PLOTCIRCOS", "octopusv", - "0.4.0 " + "0.4.0" ] ] } ], - "timestamp": "2026-07-16T10:20:39.441337134", + "timestamp": "2026-07-16T13:40:48.702498948", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" @@ -73,7 +50,7 @@ { "id": "test" }, - "test.circos.pdf:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.circos.png:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "oversized_intra": [ @@ -88,12 +65,12 @@ [ "OCTOPUSV_PLOTCIRCOS", "octopusv", - "0.4.0 " + "0.4.0" ] ] } ], - "timestamp": "2026-07-16T10:20:52.637472113", + "timestamp": "2026-07-16T13:40:58.686272993", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" From 79e6a70423a2714fb2cc28730cffda028ea55b22 Mon Sep 17 00:00:00 2001 From: manascripts Date: Mon, 20 Jul 2026 15:34:51 +0200 Subject: [PATCH 7/7] remove the version line from test --- .../nf-core/octopusv/plotcircos/tests/main.nf.test | 4 +--- .../octopusv/plotcircos/tests/main.nf.test.snap | 13 ++----------- 2 files changed, 3 insertions(+), 14 deletions(-) diff --git a/modules/nf-core/octopusv/plotcircos/tests/main.nf.test b/modules/nf-core/octopusv/plotcircos/tests/main.nf.test index 3a0dec6ccc02..97c20a6b0567 100644 --- a/modules/nf-core/octopusv/plotcircos/tests/main.nf.test +++ b/modules/nf-core/octopusv/plotcircos/tests/main.nf.test @@ -28,9 +28,7 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - sanitizeOutput(process.out), - process.out.findAll { key, val -> key.startsWith('versions') } - ).match() } + sanitizeOutput(process.out)).match() } ) } } diff --git a/modules/nf-core/octopusv/plotcircos/tests/main.nf.test.snap b/modules/nf-core/octopusv/plotcircos/tests/main.nf.test.snap index 128240e8f949..685316f6248a 100644 --- a/modules/nf-core/octopusv/plotcircos/tests/main.nf.test.snap +++ b/modules/nf-core/octopusv/plotcircos/tests/main.nf.test.snap @@ -25,18 +25,9 @@ "0.4.0" ] ] - }, - { - "versions_octopusv": [ - [ - "OCTOPUSV_PLOTCIRCOS", - "octopusv", - "0.4.0" - ] - ] } ], - "timestamp": "2026-07-16T13:40:48.702498948", + "timestamp": "2026-07-20T15:33:24.087743215", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" @@ -70,7 +61,7 @@ ] } ], - "timestamp": "2026-07-16T13:40:58.686272993", + "timestamp": "2026-07-20T15:33:32.441492316", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4"