From 0dc76417274ab9f33a5d1fef303b59025dbdc037 Mon Sep 17 00:00:00 2001 From: riccabolla Date: Sat, 25 Apr 2026 17:14:59 +0200 Subject: [PATCH 01/20] added pcne module --- modules/nf-core/pcne/environment.yml | 6 ++ modules/nf-core/pcne/main.nf | 49 ++++++++++++ modules/nf-core/pcne/meta.yml | 102 ++++++++++++++++++++++++ modules/nf-core/pcne/tests/main.nf.test | 64 +++++++++++++++ 4 files changed, 221 insertions(+) create mode 100644 modules/nf-core/pcne/environment.yml create mode 100644 modules/nf-core/pcne/main.nf create mode 100644 modules/nf-core/pcne/meta.yml create mode 100644 modules/nf-core/pcne/tests/main.nf.test diff --git a/modules/nf-core/pcne/environment.yml b/modules/nf-core/pcne/environment.yml new file mode 100644 index 00000000000..0050dff4088 --- /dev/null +++ b/modules/nf-core/pcne/environment.yml @@ -0,0 +1,6 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - "bioconda::pcne=3.3.0" \ No newline at end of file diff --git a/modules/nf-core/pcne/main.nf b/modules/nf-core/pcne/main.nf new file mode 100644 index 00000000000..2e7f173ddb3 --- /dev/null +++ b/modules/nf-core/pcne/main.nf @@ -0,0 +1,49 @@ +process PCNE { + tag "$meta.id" + label 'process_medium' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/pcne%3A3.3.0--hdfd78af_0' : + 'biocontainers/pcne:3.3.0--hdfd78af_0' }" + + input: + tuple val(meta), path(reads) + path chromosome + path plasmids + + output: + tuple val(meta), path("*_results.tsv"), emit: results + tuple val(meta), path("*.log") , emit: log + tuple val(meta), path("*.png") , emit: plots, optional: true + tuple val("${task.process}"), val('pcne'), eval("pcne -v | sed 's/.*version //'"), topic: versions, emit: versions_pcne + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + + def is_bam = reads.toString().endsWith('.bam') + def input_cmd = is_bam ? "-b ${reads}" : "-r ${reads[0]} -R ${reads[1]}" + + def plasmid_cmd = plasmids instanceof List ? plasmids.join(' ') : plasmids + + """ + pcne \\ + -c $chromosome \\ + -p $plasmid_cmd \\ + $input_cmd \\ + -o $prefix \\ + -t $task.cpus \\ + $args + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}_results.tsv + touch ${prefix}.log + """ +} \ No newline at end of file diff --git a/modules/nf-core/pcne/meta.yml b/modules/nf-core/pcne/meta.yml new file mode 100644 index 00000000000..9a2f8e35ccc --- /dev/null +++ b/modules/nf-core/pcne/meta.yml @@ -0,0 +1,102 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "pcne" +description: "Estimates plasmid copy number from assembled genome" +keywords: + - plasmid + - copy number + - genomics + - alignment + - coverage +tools: + - "pcne": + description: "Estimates plasmid copy number from assembled genome." + homepage: "https://github.com/riccabolla/PCNE" + documentation: "https://github.com/riccabolla/PCNE" + tool_dev_url: "https://github.com/riccabolla/PCNE" + doi: "10.1177/11779322251410037" + licence: ['MIT'] + identifier: "" + +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - reads: + type: file + description: FASTQ reads (paired or single) or a pre-aligned BAM file + pattern: "*.{fastq.gz,fq.gz,fastq,fq,bam}" + ontologies: + - edam: "http://edamontology.org/format_1930" # FASTQ + - edam: "http://edamontology.org/format_2572" # BAM + - - chromosome: + type: file + description: Chromosome contigs FASTA file + pattern: "*.{fasta,fa,fasta.gz,fa.gz}" + ontologies: + - edam: "http://edamontology.org/format_1929" # FASTA + - - plasmids: + type: file + description: One or more plasmid FASTA files + pattern: "*.{fasta,fa,fasta.gz,fa.gz}" + ontologies: + - edam: "http://edamontology.org/format_1929" # FASTA + +output: + results: + - - meta: + type: map + description: Groovy Map containing sample information + - "*_results.tsv": + type: file + description: TSV file containing the estimated plasmid copy numbers + pattern: "*_results.tsv" + ontologies: + - edam: "http://edamontology.org/format_3475" # TSV + log: + - - meta: + type: map + description: Groovy Map containing sample information + - "*.log": + type: file + description: PCNE run log file + pattern: "*.log" + ontologies: + - edam: "http://edamontology.org/format_2330" # Textual format + plots: + - - meta: + type: map + description: Groovy Map containing sample information + - "*.png": + type: file + description: Bar plot of plasmid copy numbers or GC vs Depth diagnostic plots + pattern: "*.png" + ontologies: + - edam: "http://edamontology.org/format_3603" # PNG + versions_pcne: + - - "${task.process}": + type: string + description: The name of the process + - "pcne": + type: string + description: The name of the tool + - "pcne -v | sed 's/.*version //'": + type: eval + description: The expression to obtain the version of the tool + +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - pcne: + type: string + description: The name of the tool + - "pcne -v | sed 's/.*version //'": + type: eval + description: The expression to obtain the version of the tool +authors: + - "@riccabolla" +maintainers: + - "@riccabolla" \ No newline at end of file diff --git a/modules/nf-core/pcne/tests/main.nf.test b/modules/nf-core/pcne/tests/main.nf.test new file mode 100644 index 00000000000..3510c795eb5 --- /dev/null +++ b/modules/nf-core/pcne/tests/main.nf.test @@ -0,0 +1,64 @@ +nextflow_process { + + name "Test Process PCNE" + script "../main.nf" + process "PCNE" + + tag "modules" + tag "modules_nfcore" + tag "pcne" + + test("sarscov2 - bam") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ] + input[1] = file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + input[2] = file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/transcriptome.fasta', checkIfExists: true) + """ + } + } + + then { + assert process.success + assertAll( + { assert snapshot(process.out.results).match("results") }, + { assert snapshot(process.out.versions_pcne).match("versions") } + ) + assert process.out.log.get(0).get(1) ==~ ".*.log" + } + + } + + test("sarscov2 - bam - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ] + input[1] = file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + input[2] = file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/transcriptome.fasta', checkIfExists: true) + """ + } + } + + then { + assert process.success + assertAll( + { assert snapshot(process.out.results).match("results_stub") }, + { assert snapshot(process.out.versions_pcne).match("versions_stub") } + ) + } + + } + +} \ No newline at end of file From 47ae1dc08da41fac0613f40c112320f4bc6b719e Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 27 Apr 2026 16:54:15 +0000 Subject: [PATCH 02/20] [automated] Fix code linting --- modules/nf-core/pcne/environment.yml | 2 +- modules/nf-core/pcne/main.nf | 8 ++++---- modules/nf-core/pcne/meta.yml | 4 ++-- modules/nf-core/pcne/tests/main.nf.test | 2 +- 4 files changed, 8 insertions(+), 8 deletions(-) diff --git a/modules/nf-core/pcne/environment.yml b/modules/nf-core/pcne/environment.yml index 0050dff4088..a133a6dcfa3 100644 --- a/modules/nf-core/pcne/environment.yml +++ b/modules/nf-core/pcne/environment.yml @@ -3,4 +3,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::pcne=3.3.0" \ No newline at end of file + - "bioconda::pcne=3.3.0" diff --git a/modules/nf-core/pcne/main.nf b/modules/nf-core/pcne/main.nf index 2e7f173ddb3..d1d3cd6c08e 100644 --- a/modules/nf-core/pcne/main.nf +++ b/modules/nf-core/pcne/main.nf @@ -5,7 +5,7 @@ process PCNE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pcne%3A3.3.0--hdfd78af_0' : - 'biocontainers/pcne:3.3.0--hdfd78af_0' }" + 'biocontainers/pcne:3.3.0--hdfd78af_0' }" input: tuple val(meta), path(reads) @@ -24,10 +24,10 @@ process PCNE { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - + def is_bam = reads.toString().endsWith('.bam') def input_cmd = is_bam ? "-b ${reads}" : "-r ${reads[0]} -R ${reads[1]}" - + def plasmid_cmd = plasmids instanceof List ? plasmids.join(' ') : plasmids """ @@ -46,4 +46,4 @@ process PCNE { touch ${prefix}_results.tsv touch ${prefix}.log """ -} \ No newline at end of file +} diff --git a/modules/nf-core/pcne/meta.yml b/modules/nf-core/pcne/meta.yml index 9a2f8e35ccc..b8a08868ab8 100644 --- a/modules/nf-core/pcne/meta.yml +++ b/modules/nf-core/pcne/meta.yml @@ -14,7 +14,7 @@ tools: documentation: "https://github.com/riccabolla/PCNE" tool_dev_url: "https://github.com/riccabolla/PCNE" doi: "10.1177/11779322251410037" - licence: ['MIT'] + licence: ["MIT"] identifier: "" input: @@ -99,4 +99,4 @@ topics: authors: - "@riccabolla" maintainers: - - "@riccabolla" \ No newline at end of file + - "@riccabolla" diff --git a/modules/nf-core/pcne/tests/main.nf.test b/modules/nf-core/pcne/tests/main.nf.test index 3510c795eb5..9ca3b16da29 100644 --- a/modules/nf-core/pcne/tests/main.nf.test +++ b/modules/nf-core/pcne/tests/main.nf.test @@ -61,4 +61,4 @@ nextflow_process { } -} \ No newline at end of file +} From ba6285f36f8d2c0b3a98dbd285b816f0f603bc7e Mon Sep 17 00:00:00 2001 From: riccabolla Date: Tue, 28 Apr 2026 13:49:51 +0200 Subject: [PATCH 03/20] Update modules/nf-core/pcne/main.nf MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> --- modules/nf-core/pcne/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/pcne/main.nf b/modules/nf-core/pcne/main.nf index d1d3cd6c08e..e9f7561d99f 100644 --- a/modules/nf-core/pcne/main.nf +++ b/modules/nf-core/pcne/main.nf @@ -5,7 +5,7 @@ process PCNE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pcne%3A3.3.0--hdfd78af_0' : - 'biocontainers/pcne:3.3.0--hdfd78af_0' }" + 'quay.io/biocontainers/pcne:3.3.0--hdfd78af_0' }" input: tuple val(meta), path(reads) From 749835e54b22befd1fb6d4a059c53c48ef52ec30 Mon Sep 17 00:00:00 2001 From: riccabolla Date: Tue, 28 Apr 2026 14:28:55 +0200 Subject: [PATCH 04/20] Refactor test assertions to use sanitized output --- modules/nf-core/pcne/tests/main.nf.test | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/modules/nf-core/pcne/tests/main.nf.test b/modules/nf-core/pcne/tests/main.nf.test index 9ca3b16da29..1534f65a8e4 100644 --- a/modules/nf-core/pcne/tests/main.nf.test +++ b/modules/nf-core/pcne/tests/main.nf.test @@ -26,8 +26,7 @@ nextflow_process { then { assert process.success assertAll( - { assert snapshot(process.out.results).match("results") }, - { assert snapshot(process.out.versions_pcne).match("versions") } + { assert snapshot(sanitizeOutput(process.out)).match() } ) assert process.out.log.get(0).get(1) ==~ ".*.log" } @@ -54,8 +53,7 @@ nextflow_process { then { assert process.success assertAll( - { assert snapshot(process.out.results).match("results_stub") }, - { assert snapshot(process.out.versions_pcne).match("versions_stub") } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } From b7bbd1df29b1210151420321b0ac05b3c3569060 Mon Sep 17 00:00:00 2001 From: riccabolla Date: Tue, 28 Apr 2026 15:04:07 +0200 Subject: [PATCH 05/20] added test snap --- modules/nf-core/pcne/tests/main.nf.test.snap | 80 ++++++++++++++++++++ 1 file changed, 80 insertions(+) create mode 100644 modules/nf-core/pcne/tests/main.nf.test.snap diff --git a/modules/nf-core/pcne/tests/main.nf.test.snap b/modules/nf-core/pcne/tests/main.nf.test.snap new file mode 100644 index 00000000000..779deae87b9 --- /dev/null +++ b/modules/nf-core/pcne/tests/main.nf.test.snap @@ -0,0 +1,80 @@ +{ + "sarscov2 - bam - stub": { + "content": [ + { + "log": [ + [ + { + "id": "test", + "single_end": false + }, + "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "plots": [ + + ], + "results": [ + [ + { + "id": "test", + "single_end": false + }, + "test_results.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_pcne": [ + [ + "PCNE", + "pcne", + " ____ ____ _ _ ____\n | _ \\ / ___| \\ | | ____|\n | |_) | | | \\| | _|\n | __/| |___| |\\ | |___\n |_| \\____|_| \\_|_____|\n Plasmid Copy Number Estimator v3.3.0\n by riccabolla\n\n3.3.0" + ] + ] + } + ], + "timestamp": "2026-04-28T14:58:52.802163553", + "meta": { + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } + }, + "sarscov2 - bam": { + "content": [ + { + "log": [ + [ + { + "id": "test", + "single_end": false + }, + "test.log:md5,b1fb98d9112135a9cfce8e0f9fdaf1d4" + ] + ], + "plots": [ + + ], + "results": [ + [ + { + "id": "test", + "single_end": false + }, + "test_results.tsv:md5,2efc4a2d2c671eeda63ce2a4aeb81fc6" + ] + ], + "versions_pcne": [ + [ + "PCNE", + "pcne", + " ____ ____ _ _ ____\n | _ \\ / ___| \\ | | ____|\n | |_) | | | \\| | _|\n | __/| |___| |\\ | |___\n |_| \\____|_| \\_|_____|\n Plasmid Copy Number Estimator v3.3.0\n by riccabolla\n\n3.3.0" + ] + ] + } + ], + "timestamp": "2026-04-28T15:02:25.298898763", + "meta": { + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } + } +} \ No newline at end of file From 8db1f55daafacec797dfa8217ec28ca14b299841 Mon Sep 17 00:00:00 2001 From: riccabolla Date: Tue, 28 Apr 2026 15:15:00 +0200 Subject: [PATCH 06/20] Update pcne version from 3.3.0 to 3.3.1 --- modules/nf-core/pcne/environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/pcne/environment.yml b/modules/nf-core/pcne/environment.yml index a133a6dcfa3..bb2a025557d 100644 --- a/modules/nf-core/pcne/environment.yml +++ b/modules/nf-core/pcne/environment.yml @@ -3,4 +3,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::pcne=3.3.0" + - "bioconda::pcne=3.3.1" From c1825c159756478ce281671b1d8db8f4b8bdd552 Mon Sep 17 00:00:00 2001 From: riccabolla Date: Tue, 28 Apr 2026 15:16:34 +0200 Subject: [PATCH 07/20] Update PCNE container version to 3.3.1 --- modules/nf-core/pcne/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/pcne/main.nf b/modules/nf-core/pcne/main.nf index e9f7561d99f..dd04be41c12 100644 --- a/modules/nf-core/pcne/main.nf +++ b/modules/nf-core/pcne/main.nf @@ -4,8 +4,8 @@ process PCNE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/pcne%3A3.3.0--hdfd78af_0' : - 'quay.io/biocontainers/pcne:3.3.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/pcne%3A3.3.1--hdfd78af_0' : + 'quay.io/biocontainers/pcne:3.3.1--hdfd78af_0' }" input: tuple val(meta), path(reads) From c86f5e7af90e310de2251d46c10bbb495bb218a5 Mon Sep 17 00:00:00 2001 From: riccabolla Date: Tue, 28 Apr 2026 15:24:34 +0200 Subject: [PATCH 08/20] fixed meta.yml --- modules/nf-core/pcne/meta.yml | 166 +++++++++++++++++----------------- 1 file changed, 82 insertions(+), 84 deletions(-) diff --git a/modules/nf-core/pcne/meta.yml b/modules/nf-core/pcne/meta.yml index b8a08868ab8..68146824944 100644 --- a/modules/nf-core/pcne/meta.yml +++ b/modules/nf-core/pcne/meta.yml @@ -1,102 +1,100 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "pcne" description: "Estimates plasmid copy number from assembled genome" keywords: - - plasmid - - copy number - - genomics - - alignment - - coverage +- plasmid +- copy number +- genomics +- alignment +- coverage tools: - - "pcne": - description: "Estimates plasmid copy number from assembled genome." - homepage: "https://github.com/riccabolla/PCNE" - documentation: "https://github.com/riccabolla/PCNE" - tool_dev_url: "https://github.com/riccabolla/PCNE" - doi: "10.1177/11779322251410037" - licence: ["MIT"] - identifier: "" - +- "pcne": + description: "Estimates plasmid copy number from assembled genome." + homepage: "https://github.com/riccabolla/PCNE" + documentation: "https://github.com/riccabolla/PCNE" + tool_dev_url: "https://github.com/riccabolla/PCNE" + doi: "10.1177/11779322251410037" + licence: + - 'MIT' + identifier: "" input: +- - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - reads: + type: file + description: FASTQ reads (paired or single) or a pre-aligned BAM file + pattern: "*.{fastq.gz,fq.gz,fastq,fq,bam}" + ontologies: + - edam: "http://edamontology.org/format_1930" + - edam: "http://edamontology.org/format_2572" +- chromosome: + type: file + description: Chromosome contigs FASTA file + pattern: "*.{fasta,fa,fasta.gz,fa.gz}" + ontologies: + - edam: "http://edamontology.org/format_1929" +- plasmids: + type: file + description: One or more plasmid FASTA files + pattern: "*.{fasta,fa,fasta.gz,fa.gz}" + ontologies: + - edam: "http://edamontology.org/format_1929" +output: + results: - - meta: type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - reads: + description: Groovy Map containing sample information + - "*_results.tsv": type: file - description: FASTQ reads (paired or single) or a pre-aligned BAM file - pattern: "*.{fastq.gz,fq.gz,fastq,fq,bam}" + description: TSV file containing the estimated plasmid copy numbers + pattern: "*_results.tsv" ontologies: - - edam: "http://edamontology.org/format_1930" # FASTQ - - edam: "http://edamontology.org/format_2572" # BAM - - - chromosome: + - edam: "http://edamontology.org/format_3475" + log: + - - meta: + type: map + description: Groovy Map containing sample information + - "*.log": type: file - description: Chromosome contigs FASTA file - pattern: "*.{fasta,fa,fasta.gz,fa.gz}" + description: PCNE run log file + pattern: "*.log" ontologies: - - edam: "http://edamontology.org/format_1929" # FASTA - - - plasmids: + - edam: "http://edamontology.org/format_2330" + plots: + - - meta: + type: map + description: Groovy Map containing sample information + - "*.png": type: file - description: One or more plasmid FASTA files - pattern: "*.{fasta,fa,fasta.gz,fa.gz}" + description: Bar plot of plasmid copy numbers or GC vs Depth diagnostic + plots + pattern: "*.png" ontologies: - - edam: "http://edamontology.org/format_1929" # FASTA - -output: - results: - - - meta: - type: map - description: Groovy Map containing sample information - - "*_results.tsv": - type: file - description: TSV file containing the estimated plasmid copy numbers - pattern: "*_results.tsv" - ontologies: - - edam: "http://edamontology.org/format_3475" # TSV - log: - - - meta: - type: map - description: Groovy Map containing sample information - - "*.log": - type: file - description: PCNE run log file - pattern: "*.log" - ontologies: - - edam: "http://edamontology.org/format_2330" # Textual format - plots: - - - meta: - type: map - description: Groovy Map containing sample information - - "*.png": - type: file - description: Bar plot of plasmid copy numbers or GC vs Depth diagnostic plots - pattern: "*.png" - ontologies: - - edam: "http://edamontology.org/format_3603" # PNG + - edam: "http://edamontology.org/format_3603" versions_pcne: - - - "${task.process}": - type: string - description: The name of the process - - "pcne": - type: string - description: The name of the tool - - "pcne -v | sed 's/.*version //'": - type: eval - description: The expression to obtain the version of the tool - + - - "${task.process}": + type: string + description: The name of the process + - "pcne": + type: string + description: The name of the tool + - "pcne -v | sed 's/.*version //'": + type: eval + description: The expression to obtain the version of the tool topics: versions: - - - ${task.process}: - type: string - description: The name of the process - - pcne: - type: string - description: The name of the tool - - "pcne -v | sed 's/.*version //'": - type: eval - description: The expression to obtain the version of the tool + - - "${task.process}": + type: string + description: The name of the process + - "pcne": + type: string + description: The name of the tool + - "pcne -v | sed 's/.*version //'": + type: eval + description: The expression to obtain the version of the tool authors: - - "@riccabolla" +- "@riccabolla" maintainers: - - "@riccabolla" +- "@riccabolla" From 1ec3b0e623f8e7268c6f1bd1c0ee137468da68b8 Mon Sep 17 00:00:00 2001 From: riccabolla Date: Tue, 28 Apr 2026 16:49:26 +0200 Subject: [PATCH 09/20] Refactor input structure in meta.yml for clarity --- modules/nf-core/pcne/meta.yml | 58 ++++++++++++++++++++--------------- 1 file changed, 34 insertions(+), 24 deletions(-) diff --git a/modules/nf-core/pcne/meta.yml b/modules/nf-core/pcne/meta.yml index 68146824944..3f042feb7f7 100644 --- a/modules/nf-core/pcne/meta.yml +++ b/modules/nf-core/pcne/meta.yml @@ -17,30 +17,40 @@ tools: - 'MIT' identifier: "" input: -- - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - reads: - type: file - description: FASTQ reads (paired or single) or a pre-aligned BAM file - pattern: "*.{fastq.gz,fq.gz,fastq,fq,bam}" - ontologies: - - edam: "http://edamontology.org/format_1930" - - edam: "http://edamontology.org/format_2572" -- chromosome: - type: file - description: Chromosome contigs FASTA file - pattern: "*.{fasta,fa,fasta.gz,fa.gz}" - ontologies: - - edam: "http://edamontology.org/format_1929" -- plasmids: - type: file - description: One or more plasmid FASTA files - pattern: "*.{fasta,fa,fasta.gz,fa.gz}" - ontologies: - - edam: "http://edamontology.org/format_1929" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - reads: + type: file + description: FASTQ reads (paired or single) or a pre-aligned BAM file + pattern: "*.{fastq.gz,fq.gz,fastq,fq,bam}" + ontologies: + - edam: "http://edamontology.org/format_1930" # FASTQ + - edam: "http://edamontology.org/format_2572" # BAM + - - meta2: + type: map + description: | + Groovy Map containing reference chromosome information + e.g. `[ id:'genome' ]` + - chromosome: + type: file + description: Chromosome contigs FASTA file + pattern: "*.{fasta,fa,fasta.gz,fa.gz}" + ontologies: + - edam: "http://edamontology.org/format_1929" # FASTA + - - meta3: + type: map + description: | + Groovy Map containing reference plasmid information + e.g. `[ id:'plasmids' ]` + - plasmids: + type: file + description: One or more plasmid FASTA files + pattern: "*.{fasta,fa,fasta.gz,fa.gz}" + ontologies: + - edam: "http://edamontology.org/format_1929" # FASTA output: results: - - meta: From 30452f8f6bec51a07cacdf5aa6c933079685120a Mon Sep 17 00:00:00 2001 From: riccabolla Date: Tue, 28 Apr 2026 16:50:04 +0200 Subject: [PATCH 10/20] Refactor PCNE process for improved readability --- modules/nf-core/pcne/main.nf | 30 +++++++++++++++--------------- 1 file changed, 15 insertions(+), 15 deletions(-) diff --git a/modules/nf-core/pcne/main.nf b/modules/nf-core/pcne/main.nf index dd04be41c12..8e8e5d4904c 100644 --- a/modules/nf-core/pcne/main.nf +++ b/modules/nf-core/pcne/main.nf @@ -1,21 +1,21 @@ process PCNE { - tag "$meta.id" + tag "${meta.id}" label 'process_medium' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/pcne%3A3.3.1--hdfd78af_0' : - 'quay.io/biocontainers/pcne:3.3.1--hdfd78af_0' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://depot.galaxyproject.org/singularity/pcne%3A3.3.1--hdfd78af_0' + : 'quay.io/biocontainers/pcne:3.3.1--hdfd78af_0' }" input: tuple val(meta), path(reads) - path chromosome - path plasmids + tuple val(meta2), path(chromosome) + tuple val(meta3), path(plasmids) output: tuple val(meta), path("*_results.tsv"), emit: results - tuple val(meta), path("*.log") , emit: log - tuple val(meta), path("*.png") , emit: plots, optional: true + tuple val(meta), path("*.log"), emit: log + tuple val(meta), path("*.png"), emit: plots, optional: true tuple val("${task.process}"), val('pcne'), eval("pcne -v | sed 's/.*version //'"), topic: versions, emit: versions_pcne when: @@ -25,19 +25,19 @@ process PCNE { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def is_bam = reads.toString().endsWith('.bam') + def is_bam = reads.toString().endsWith('.bam') def input_cmd = is_bam ? "-b ${reads}" : "-r ${reads[0]} -R ${reads[1]}" def plasmid_cmd = plasmids instanceof List ? plasmids.join(' ') : plasmids """ pcne \\ - -c $chromosome \\ - -p $plasmid_cmd \\ - $input_cmd \\ - -o $prefix \\ - -t $task.cpus \\ - $args + -c ${chromosome} \\ + -p ${plasmid_cmd} \\ + ${input_cmd} \\ + -o ${prefix} \\ + -t ${task.cpus} \\ + ${args} """ stub: From 4c8aaa7b9de2c5a1d80c696e165d22d657b7d6f9 Mon Sep 17 00:00:00 2001 From: riccabolla Date: Tue, 28 Apr 2026 16:50:49 +0200 Subject: [PATCH 11/20] Update PCNE version from 3.3.0 to 3.3.1 --- modules/nf-core/pcne/tests/main.nf.test.snap | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/modules/nf-core/pcne/tests/main.nf.test.snap b/modules/nf-core/pcne/tests/main.nf.test.snap index 779deae87b9..28742c034c1 100644 --- a/modules/nf-core/pcne/tests/main.nf.test.snap +++ b/modules/nf-core/pcne/tests/main.nf.test.snap @@ -27,12 +27,12 @@ [ "PCNE", "pcne", - " ____ ____ _ _ ____\n | _ \\ / ___| \\ | | ____|\n | |_) | | | \\| | _|\n | __/| |___| |\\ | |___\n |_| \\____|_| \\_|_____|\n Plasmid Copy Number Estimator v3.3.0\n by riccabolla\n\n3.3.0" + " ____ ____ _ _ ____\n | _ \\ / ___| \\ | | ____|\n | |_) | | | \\| | _|\n | __/| |___| |\\ | |___\n |_| \\____|_| \\_|_____|\n Plasmid Copy Number Estimator v3.3.1\n by riccabolla\n\n3.3.1" ] ] } ], - "timestamp": "2026-04-28T14:58:52.802163553", + "timestamp": "2026-04-28T15:41:35.79438613", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" @@ -47,7 +47,7 @@ "id": "test", "single_end": false }, - "test.log:md5,b1fb98d9112135a9cfce8e0f9fdaf1d4" + "test.log:md5,e9efe6d2a532c46bffca00a1ba8a8b92" ] ], "plots": [ @@ -66,15 +66,15 @@ [ "PCNE", "pcne", - " ____ ____ _ _ ____\n | _ \\ / ___| \\ | | ____|\n | |_) | | | \\| | _|\n | __/| |___| |\\ | |___\n |_| \\____|_| \\_|_____|\n Plasmid Copy Number Estimator v3.3.0\n by riccabolla\n\n3.3.0" + " ____ ____ _ _ ____\n | _ \\ / ___| \\ | | ____|\n | |_) | | | \\| | _|\n | __/| |___| |\\ | |___\n |_| \\____|_| \\_|_____|\n Plasmid Copy Number Estimator v3.3.1\n by riccabolla\n\n3.3.1" ] ] } ], - "timestamp": "2026-04-28T15:02:25.298898763", + "timestamp": "2026-04-28T15:41:18.160584917", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" } } -} \ No newline at end of file +} From f505ea04e686eb4361ad4bd36ebce4266f2ba0aa Mon Sep 17 00:00:00 2001 From: riccabolla Date: Tue, 28 Apr 2026 17:05:16 +0200 Subject: [PATCH 12/20] Update test inputs to use module test data paths --- modules/nf-core/pcne/tests/main.nf.test | 33 +++++++++++++++---------- 1 file changed, 20 insertions(+), 13 deletions(-) diff --git a/modules/nf-core/pcne/tests/main.nf.test b/modules/nf-core/pcne/tests/main.nf.test index 1534f65a8e4..70562b53c5d 100644 --- a/modules/nf-core/pcne/tests/main.nf.test +++ b/modules/nf-core/pcne/tests/main.nf.test @@ -15,20 +15,23 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) ] - input[1] = file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - input[2] = file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/transcriptome.fasta', checkIfExists: true) + input[1] = [ + [ id: 'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ + [ id: 'transcriptome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/transcriptome.fasta', checkIfExists: true) + ] """ } } then { assert process.success - assertAll( - { assert snapshot(sanitizeOutput(process.out)).match() } - ) - assert process.out.log.get(0).get(1) ==~ ".*.log" + assert snapshot(sanitizeOutput(process.out)).match() } } @@ -42,19 +45,23 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) ] - input[1] = file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - input[2] = file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/transcriptome.fasta', checkIfExists: true) + input[1] = [ + [ id: 'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ + [ id: 'transcriptome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/transcriptome.fasta', checkIfExists: true) + ] """ } } then { assert process.success - assertAll( - { assert snapshot(sanitizeOutput(process.out)).match() } - ) + assert snapshot(sanitizeOutput(process.out)).match() } } From cd1f842fccedf446e16cd2d9a4125a5a3dff4ec1 Mon Sep 17 00:00:00 2001 From: riccabolla Date: Tue, 28 Apr 2026 17:21:15 +0200 Subject: [PATCH 13/20] whitespace fixing Corrected indentation for description field in meta.yml. --- modules/nf-core/pcne/meta.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/pcne/meta.yml b/modules/nf-core/pcne/meta.yml index 3f042feb7f7..b2ebef167c0 100644 --- a/modules/nf-core/pcne/meta.yml +++ b/modules/nf-core/pcne/meta.yml @@ -78,7 +78,7 @@ output: description: Groovy Map containing sample information - "*.png": type: file - description: Bar plot of plasmid copy numbers or GC vs Depth diagnostic + description: Bar plot of plasmid copy numbers or GC vs Depth diagnostic plots pattern: "*.png" ontologies: From 9728f9ad32dfd56f93151cb966ac1f0e88b456a6 Mon Sep 17 00:00:00 2001 From: riccabolla Date: Tue, 28 Apr 2026 17:22:06 +0200 Subject: [PATCH 14/20] Fix input array formatting in main.nf.test --- modules/nf-core/pcne/tests/main.nf.test | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/modules/nf-core/pcne/tests/main.nf.test b/modules/nf-core/pcne/tests/main.nf.test index 70562b53c5d..29471059bc3 100644 --- a/modules/nf-core/pcne/tests/main.nf.test +++ b/modules/nf-core/pcne/tests/main.nf.test @@ -20,11 +20,11 @@ nextflow_process { input[1] = [ [ id: 'genome' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ] + ] input[2] = [ [ id: 'transcriptome' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/transcriptome.fasta', checkIfExists: true) - ] + ] """ } } @@ -50,11 +50,11 @@ nextflow_process { input[1] = [ [ id: 'genome' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ] + ] input[2] = [ [ id: 'transcriptome' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/transcriptome.fasta', checkIfExists: true) - ] + ] """ } } From 73d9715d592e7aef465960dd4fa6861f07183dfe Mon Sep 17 00:00:00 2001 From: riccabolla Date: Wed, 29 Apr 2026 11:21:59 +0200 Subject: [PATCH 15/20] fixed to pass pre-commit formatted to pass prettier check --- modules/nf-core/pcne/meta.yml | 124 +++++++++++++++++----------------- 1 file changed, 62 insertions(+), 62 deletions(-) diff --git a/modules/nf-core/pcne/meta.yml b/modules/nf-core/pcne/meta.yml index b2ebef167c0..936f318d47a 100644 --- a/modules/nf-core/pcne/meta.yml +++ b/modules/nf-core/pcne/meta.yml @@ -1,21 +1,21 @@ name: "pcne" description: "Estimates plasmid copy number from assembled genome" keywords: -- plasmid -- copy number -- genomics -- alignment -- coverage + - plasmid + - copy number + - genomics + - alignment + - coverage tools: -- "pcne": - description: "Estimates plasmid copy number from assembled genome." - homepage: "https://github.com/riccabolla/PCNE" - documentation: "https://github.com/riccabolla/PCNE" - tool_dev_url: "https://github.com/riccabolla/PCNE" - doi: "10.1177/11779322251410037" - licence: - - 'MIT' - identifier: "" + - "pcne": + description: "Estimates plasmid copy number from assembled genome." + homepage: "https://github.com/riccabolla/PCNE" + documentation: "https://github.com/riccabolla/PCNE" + tool_dev_url: "https://github.com/riccabolla/PCNE" + doi: "10.1177/11779322251410037" + licence: + - "MIT" + identifier: "" input: - - meta: type: map @@ -53,58 +53,58 @@ input: - edam: "http://edamontology.org/format_1929" # FASTA output: results: - - - meta: - type: map - description: Groovy Map containing sample information - - "*_results.tsv": - type: file - description: TSV file containing the estimated plasmid copy numbers - pattern: "*_results.tsv" - ontologies: - - edam: "http://edamontology.org/format_3475" + - - meta: + type: map + description: Groovy Map containing sample information + - "*_results.tsv": + type: file + description: TSV file containing the estimated plasmid copy numbers + pattern: "*_results.tsv" + ontologies: + - edam: "http://edamontology.org/format_3475" log: - - - meta: - type: map - description: Groovy Map containing sample information - - "*.log": - type: file - description: PCNE run log file - pattern: "*.log" - ontologies: - - edam: "http://edamontology.org/format_2330" + - - meta: + type: map + description: Groovy Map containing sample information + - "*.log": + type: file + description: PCNE run log file + pattern: "*.log" + ontologies: + - edam: "http://edamontology.org/format_2330" plots: - - - meta: - type: map - description: Groovy Map containing sample information - - "*.png": - type: file - description: Bar plot of plasmid copy numbers or GC vs Depth diagnostic - plots - pattern: "*.png" - ontologies: - - edam: "http://edamontology.org/format_3603" + - - meta: + type: map + description: Groovy Map containing sample information + - "*.png": + type: file + description: Bar plot of plasmid copy numbers or GC vs Depth diagnostic + plots + pattern: "*.png" + ontologies: + - edam: "http://edamontology.org/format_3603" versions_pcne: - - - "${task.process}": - type: string - description: The name of the process - - "pcne": - type: string - description: The name of the tool - - "pcne -v | sed 's/.*version //'": - type: eval - description: The expression to obtain the version of the tool + - - "${task.process}": + type: string + description: The name of the process + - "pcne": + type: string + description: The name of the tool + - "pcne -v | sed 's/.*version //'": + type: eval + description: The expression to obtain the version of the tool topics: versions: - - - "${task.process}": - type: string - description: The name of the process - - "pcne": - type: string - description: The name of the tool - - "pcne -v | sed 's/.*version //'": - type: eval - description: The expression to obtain the version of the tool + - - "${task.process}": + type: string + description: The name of the process + - "pcne": + type: string + description: The name of the tool + - "pcne -v | sed 's/.*version //'": + type: eval + description: The expression to obtain the version of the tool authors: -- "@riccabolla" + - "@riccabolla" maintainers: -- "@riccabolla" + - "@riccabolla" From 4a998d7c941770e4e1f99608aed0fc23a122bcec Mon Sep 17 00:00:00 2001 From: riccabolla Date: Wed, 29 Apr 2026 12:02:37 +0200 Subject: [PATCH 16/20] Update meta.yaml to match new version check in main.nf --- modules/nf-core/pcne/meta.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/pcne/meta.yml b/modules/nf-core/pcne/meta.yml index 936f318d47a..21e44a49199 100644 --- a/modules/nf-core/pcne/meta.yml +++ b/modules/nf-core/pcne/meta.yml @@ -90,7 +90,7 @@ output: - "pcne": type: string description: The name of the tool - - "pcne -v | sed 's/.*version //'": + - "pcne -v | grep 'version' | tail -n 1 | sed 's/.*version //'": type: eval description: The expression to obtain the version of the tool topics: From 6a46974e0d50b7a8468792074ba59d60ec3c827f Mon Sep 17 00:00:00 2001 From: riccabolla Date: Wed, 29 Apr 2026 12:03:04 +0200 Subject: [PATCH 17/20] Update version extraction command for pcne --- modules/nf-core/pcne/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/pcne/main.nf b/modules/nf-core/pcne/main.nf index 8e8e5d4904c..df273e52797 100644 --- a/modules/nf-core/pcne/main.nf +++ b/modules/nf-core/pcne/main.nf @@ -16,7 +16,7 @@ process PCNE { tuple val(meta), path("*_results.tsv"), emit: results tuple val(meta), path("*.log"), emit: log tuple val(meta), path("*.png"), emit: plots, optional: true - tuple val("${task.process}"), val('pcne'), eval("pcne -v | sed 's/.*version //'"), topic: versions, emit: versions_pcne + tuple val("${task.process}"), val('pcne'), eval("pcne -v | grep 'version' | tail -n 1 | sed 's/.*version //'"), topic: versions, emit: versions_pcne when: task.ext.when == null || task.ext.when From f7e006210cb0b8a24a9ec20e9cc2aa995b24a403 Mon Sep 17 00:00:00 2001 From: riccabolla Date: Wed, 29 Apr 2026 12:41:46 +0200 Subject: [PATCH 18/20] Fix indentation and update ontology references in meta.yml --- modules/nf-core/pcne/meta.yml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/modules/nf-core/pcne/meta.yml b/modules/nf-core/pcne/meta.yml index 21e44a49199..38d1e311b1e 100644 --- a/modules/nf-core/pcne/meta.yml +++ b/modules/nf-core/pcne/meta.yml @@ -27,8 +27,8 @@ input: description: FASTQ reads (paired or single) or a pre-aligned BAM file pattern: "*.{fastq.gz,fq.gz,fastq,fq,bam}" ontologies: - - edam: "http://edamontology.org/format_1930" # FASTQ - - edam: "http://edamontology.org/format_2572" # BAM + - edam: "http://edamontology.org/format_1930" + - edam: "http://edamontology.org/format_2572" - - meta2: type: map description: | @@ -39,7 +39,7 @@ input: description: Chromosome contigs FASTA file pattern: "*.{fasta,fa,fasta.gz,fa.gz}" ontologies: - - edam: "http://edamontology.org/format_1929" # FASTA + - edam: "http://edamontology.org/format_1929" - - meta3: type: map description: | @@ -50,7 +50,7 @@ input: description: One or more plasmid FASTA files pattern: "*.{fasta,fa,fasta.gz,fa.gz}" ontologies: - - edam: "http://edamontology.org/format_1929" # FASTA + - edam: "http://edamontology.org/format_1929" output: results: - - meta: @@ -101,7 +101,7 @@ topics: - "pcne": type: string description: The name of the tool - - "pcne -v | sed 's/.*version //'": + - "pcne -v | grep 'version' | tail -n 1 | sed 's/.*version //'": type: eval description: The expression to obtain the version of the tool authors: From 70940187f71d19c588aa7bc70abf21ff6acc41dd Mon Sep 17 00:00:00 2001 From: riccabolla Date: Wed, 29 Apr 2026 12:46:55 +0200 Subject: [PATCH 19/20] fixed snap version output --- modules/nf-core/pcne/tests/main.nf.test.snap | 92 +++++++------------- 1 file changed, 32 insertions(+), 60 deletions(-) diff --git a/modules/nf-core/pcne/tests/main.nf.test.snap b/modules/nf-core/pcne/tests/main.nf.test.snap index 28742c034c1..c26a0371e5e 100644 --- a/modules/nf-core/pcne/tests/main.nf.test.snap +++ b/modules/nf-core/pcne/tests/main.nf.test.snap @@ -1,38 +1,24 @@ { "sarscov2 - bam - stub": { "content": [ - { - "log": [ - [ - { - "id": "test", - "single_end": false - }, - "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "plots": [ - - ], - "results": [ - [ - { - "id": "test", - "single_end": false - }, - "test_results.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions_pcne": [ - [ - "PCNE", - "pcne", - " ____ ____ _ _ ____\n | _ \\ / ___| \\ | | ____|\n | |_) | | | \\| | _|\n | __/| |___| |\\ | |___\n |_| \\____|_| \\_|_____|\n Plasmid Copy Number Estimator v3.3.1\n by riccabolla\n\n3.3.1" - ] + [ + [ + { + "id": "test", + "single_end": false + }, + "test_results.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ] - } + ], + [ + [ + "PCNE", + "pcne", + "3.3.1" + ] + ] ], - "timestamp": "2026-04-28T15:41:35.79438613", + "timestamp": "2026-04-29T12:00:04.673689152", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" @@ -40,38 +26,24 @@ }, "sarscov2 - bam": { "content": [ - { - "log": [ - [ - { - "id": "test", - "single_end": false - }, - "test.log:md5,e9efe6d2a532c46bffca00a1ba8a8b92" - ] - ], - "plots": [ - - ], - "results": [ - [ - { - "id": "test", - "single_end": false - }, - "test_results.tsv:md5,2efc4a2d2c671eeda63ce2a4aeb81fc6" - ] - ], - "versions_pcne": [ - [ - "PCNE", - "pcne", - " ____ ____ _ _ ____\n | _ \\ / ___| \\ | | ____|\n | |_) | | | \\| | _|\n | __/| |___| |\\ | |___\n |_| \\____|_| \\_|_____|\n Plasmid Copy Number Estimator v3.3.1\n by riccabolla\n\n3.3.1" - ] + [ + [ + { + "id": "test", + "single_end": false + }, + "test_results.tsv:md5,2efc4a2d2c671eeda63ce2a4aeb81fc6" + ] + ], + [ + [ + "PCNE", + "pcne", + "3.3.1" ] - } + ] ], - "timestamp": "2026-04-28T15:41:18.160584917", + "timestamp": "2026-04-29T11:59:47.481309487", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" From decbceb5a48a42b1eb458c39091faccdc445a1fd Mon Sep 17 00:00:00 2001 From: riccabolla Date: Wed, 29 Apr 2026 17:22:07 +0200 Subject: [PATCH 20/20] test snap --- modules/nf-core/pcne/tests/main.nf.test.snap | 92 +++++++++++++------- 1 file changed, 60 insertions(+), 32 deletions(-) diff --git a/modules/nf-core/pcne/tests/main.nf.test.snap b/modules/nf-core/pcne/tests/main.nf.test.snap index c26a0371e5e..bb13c563247 100644 --- a/modules/nf-core/pcne/tests/main.nf.test.snap +++ b/modules/nf-core/pcne/tests/main.nf.test.snap @@ -1,24 +1,38 @@ { "sarscov2 - bam - stub": { "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, - "test_results.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + { + "log": [ + [ + { + "id": "test", + "single_end": false + }, + "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "plots": [ + + ], + "results": [ + [ + { + "id": "test", + "single_end": false + }, + "test_results.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_pcne": [ + [ + "PCNE", + "pcne", + "3.3.1" + ] ] - ], - [ - [ - "PCNE", - "pcne", - "3.3.1" - ] - ] + } ], - "timestamp": "2026-04-29T12:00:04.673689152", + "timestamp": "2026-04-29T17:10:13.997705663", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" @@ -26,24 +40,38 @@ }, "sarscov2 - bam": { "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, - "test_results.tsv:md5,2efc4a2d2c671eeda63ce2a4aeb81fc6" - ] - ], - [ - [ - "PCNE", - "pcne", - "3.3.1" + { + "log": [ + [ + { + "id": "test", + "single_end": false + }, + "test.log:md5,9b282212a32df78088bdcb7a173df4ce" + ] + ], + "plots": [ + + ], + "results": [ + [ + { + "id": "test", + "single_end": false + }, + "test_results.tsv:md5,2efc4a2d2c671eeda63ce2a4aeb81fc6" + ] + ], + "versions_pcne": [ + [ + "PCNE", + "pcne", + "3.3.1" + ] ] - ] + } ], - "timestamp": "2026-04-29T11:59:47.481309487", + "timestamp": "2026-04-29T17:09:56.768899583", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4"