From fb63cbf0f3beb431d53093457bbc434b1bb6fb43 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 10 Jul 2025 16:19:11 +0200 Subject: [PATCH 1/3] update workflow-output-defs to 25.04.0 --- .github/workflows/ci.yml | 4 +- README.md | 2 +- main.nf | 100 ++++++++++++++++++--------------------- nextflow.config | 2 +- 4 files changed, 51 insertions(+), 57 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 752463c4..cf01a50d 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -21,7 +21,7 @@ concurrency: cancel-in-progress: true jobs: - test_all: + test: name: Run nf-test with ${{ matrix.test }}-${{ matrix.NXF_VER }} # Only run on push if this is the nf-core dev branch (merged PRs) if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-cmgg/structural') }}" @@ -29,7 +29,7 @@ jobs: strategy: matrix: NXF_VER: - - "24.10.0" + - "25.04.0" - "latest-everything" test: - "pipeline_sv" diff --git a/README.md b/README.md index 9d76527a..87808845 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,7 @@ [![GitHub Actions Linting Status](https://github.com/nf-cmgg/structural/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-cmgg/structural/actions/workflows/linting.yml)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) -[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.10.0-23aa62.svg)](https://www.nextflow.io/) +[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A525.04.0-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) diff --git a/main.nf b/main.nf index 70109204..065e57f2 100644 --- a/main.nf +++ b/main.nf @@ -128,74 +128,68 @@ workflow { ) publish: - STRUCTURAL.out.caller_vcfs >> 'caller_vcfs' - STRUCTURAL.out.sample_vcfs >> 'sample_vcfs' - STRUCTURAL.out.family_vcfs >> 'family_vcfs' - STRUCTURAL.out.qdnaseq_out >> 'qdnaseq_out' - STRUCTURAL.out.wisecondorx_out >> 'wisecondorx_out' - STRUCTURAL.out.bedpe >> 'bedpe' - STRUCTURAL.out.multiqc_report >> 'multiqc' - STRUCTURAL.out.multiqc_data >> 'multiqc_data' + caller_vcfs = STRUCTURAL.out.caller_vcfs + sample_vcfs = STRUCTURAL.out.sample_vcfs + family_vcfs = STRUCTURAL.out.family_vcfs + qdnaseq_out = STRUCTURAL.out.qdnaseq_out + wisecondorx_out = STRUCTURAL.out.wisecondorx_out + bedpe = STRUCTURAL.out.bedpe + multiqc = STRUCTURAL.out.multiqc_report + multiqc_data = STRUCTURAL.out.multiqc_data } output { - 'caller_vcfs' { + caller_vcfs { enabled params.output_callers - path { meta, vcf, _tbi -> { file -> - if(file == vcf.name) { - return "${meta.sample}/${meta.caller}/${meta.sample}.vcf.gz" - } - return "${meta.sample}/${meta.caller}/${meta.sample}.vcf.gz.tbi" - } } + path { meta, vcf, tbi -> + vcf >> "${meta.sample}/${meta.caller}/${meta.sample}.vcf.gz" + tbi >> "${meta.sample}/${meta.caller}/${meta.sample}.vcf.gz.tbi" + } } - 'sample_vcfs' { - path { meta, vcf, _tbi -> { file -> + sample_vcfs { + path { meta, vcf, tbi -> def base = "${meta.id}/${meta.id}${meta.variant_type ? '.' + meta.variant_type : ''}" - if(file == vcf.name) { - return "${base}.vcf.gz" - } - return "${base}.vcf.gz.tbi" - } } + vcf >> "${base}.vcf.gz" + tbi >> "${base}.vcf.gz.tbi" + } } - 'family_vcfs' { - path { meta, vcf, _tbi -> { file -> + family_vcfs { + path { meta, vcf, tbi -> def base = "${meta.id}/${meta.id}${meta.variant_type ? '.' + meta.variant_type : ''}" - if(file == vcf.name) { - return "${base}.vcf.gz" - } - return "${base}.vcf.gz.tbi" - } } + vcf >> "${base}.vcf.gz" + tbi >> "${base}.vcf.gz.tbi" + } } - 'qdnaseq_out' { - path { meta, _bed -> { file -> - if(file == "statistics.out") { - return "${meta.id}/${meta.id}.qdnaseq.statistics.out" - } - def new_name = file.replaceFirst(meta.id, "${meta.id}.qdnaseq") - return "${meta.id}/${new_name}" - } } + qdnaseq_out { + path { meta, _bed_qdnaseq -> "$meta.id/qdnaseq/" + // def base_suffix = bed_qdnaseq.name.replace(meta.id, "${meta.id}.qdnaseq") + // bed_qdnaseq >> bed_qdnaseq.name == "statistics.out" ? + // "${meta.id}/${meta.id}.qdnaseq.statistics.out" : + // "${meta.id}/${base_suffix}" + } } - 'wisecondorx_out' { - path { meta, _bed -> { file -> - if(file.endsWith(".png")) { - return "${meta.id}/${meta.id}.wisecondorx.${file}" - } - def new_name = file.replaceFirst(meta.id, "${meta.id}.wisecondorx") - return "${meta.id}/${new_name}" - } } + wisecondorx_out { + path { meta, _bed -> "$meta.id/wisecondorx/" + // if(bed.name.endsWith(".png")) { + // bed >> "${meta.id}/${meta.id}.wisecondorx.${bed.name}" + // } else { + // def new_name = bed.name.replaceFirst(meta.id, "${meta.id}.wisecondorx") + // bed >> "${meta.id}/${new_name}" + // } + } } - 'bedpe' { - path { meta, _bedpe -> { file -> + bedpe { + path { meta, bedpe -> def base = "${meta.id}/${meta.id}${meta.variant_type ? '.' + meta.variant_type : ''}" - return "${base}.bedpe" - } } + bedpe >> "${base}.bedpe" + } } - 'multiqc' { - path { _report -> { _file -> "multiqc/multiqc_report.html"}} + multiqc { + path { "multiqc/" } } - 'multiqc_data' { - path { _folder -> { _file -> "multiqc/multiqc_data"}} + multiqc_data { + path { "multiqc/" } } } diff --git a/nextflow.config b/nextflow.config index 65038688..52c6bef7 100644 --- a/nextflow.config +++ b/nextflow.config @@ -279,7 +279,7 @@ manifest { description = """A bioinformatics best-practice analysis pipeline for calling structural variants (SVs), copy number variants (CNVs) and repeat region expansions (RREs) from short DNA reads.""" mainScript = 'main.nf' defaultBranch = 'main' - nextflowVersion = '!>=24.10.0' + nextflowVersion = '!>=25.04.0' version = '0.3.0dev' doi = '' } From 37f09bf6a5475cdcae88655df3d72686743fa3a5 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 10 Jul 2025 16:33:53 +0200 Subject: [PATCH 2/3] update tests --- tests/pipeline/all_types/all.nf.test.snap | 258 ++++++++--------- tests/pipeline/cnv/cnv.nf.test.snap | 116 ++++---- .../duplicates/duplicates.nf.test.snap | 34 +-- tests/pipeline/families/families.nf.test.snap | 264 +++++++++--------- 4 files changed, 336 insertions(+), 336 deletions(-) diff --git a/tests/pipeline/all_types/all.nf.test.snap b/tests/pipeline/all_types/all.nf.test.snap index 192d8d5f..e8904933 100644 --- a/tests/pipeline/all_types/all.nf.test.snap +++ b/tests/pipeline/all_types/all.nf.test.snap @@ -7,77 +7,77 @@ [ "PosCon1/PosCon1.cnv.vcf.gz", "PosCon1/PosCon1.cnv.vcf.gz.tbi", - "PosCon1/PosCon1.qdnaseq.qdnaseq.bed", - "PosCon1/PosCon1.qdnaseq.qdnaseq_segments.txt", - "PosCon1/PosCon1.qdnaseq.statistics.out", "PosCon1/PosCon1.repeats.vcf.gz", "PosCon1/PosCon1.repeats.vcf.gz.tbi", "PosCon1/PosCon1.sv.vcf.gz", "PosCon1/PosCon1.sv.vcf.gz.tbi", - "PosCon1/PosCon1.wisecondorx.chr1.png", - "PosCon1/PosCon1.wisecondorx.chr22.png", - "PosCon1/PosCon1.wisecondorx.genome_wide.png", - "PosCon1/PosCon1.wisecondorx.wisecondorx_aberrations.bed", - "PosCon1/PosCon1.wisecondorx.wisecondorx_bins.bed", - "PosCon1/PosCon1.wisecondorx.wisecondorx_segments.bed", - "PosCon1/PosCon1.wisecondorx.wisecondorx_statistics.txt", + "PosCon1/qdnaseq/PosCon1.qdnaseq.bed", + "PosCon1/qdnaseq/PosCon1.qdnaseq_segments.txt", + "PosCon1/qdnaseq/statistics.out", + "PosCon1/wisecondorx/PosCon1.wisecondorx_aberrations.bed", + "PosCon1/wisecondorx/PosCon1.wisecondorx_bins.bed", + "PosCon1/wisecondorx/PosCon1.wisecondorx_segments.bed", + "PosCon1/wisecondorx/PosCon1.wisecondorx_statistics.txt", + "PosCon1/wisecondorx/chr1.png", + "PosCon1/wisecondorx/chr22.png", + "PosCon1/wisecondorx/genome_wide.png", "PosCon2/PosCon2.cnv.vcf.gz", "PosCon2/PosCon2.cnv.vcf.gz.tbi", - "PosCon2/PosCon2.qdnaseq.qdnaseq.bed", - "PosCon2/PosCon2.qdnaseq.qdnaseq_segments.txt", - "PosCon2/PosCon2.qdnaseq.statistics.out", "PosCon2/PosCon2.repeats.vcf.gz", "PosCon2/PosCon2.repeats.vcf.gz.tbi", "PosCon2/PosCon2.sv.vcf.gz", "PosCon2/PosCon2.sv.vcf.gz.tbi", - "PosCon2/PosCon2.wisecondorx.chr1.png", - "PosCon2/PosCon2.wisecondorx.chr22.png", - "PosCon2/PosCon2.wisecondorx.genome_wide.png", - "PosCon2/PosCon2.wisecondorx.wisecondorx_aberrations.bed", - "PosCon2/PosCon2.wisecondorx.wisecondorx_bins.bed", - "PosCon2/PosCon2.wisecondorx.wisecondorx_segments.bed", - "PosCon2/PosCon2.wisecondorx.wisecondorx_statistics.txt", + "PosCon2/qdnaseq/PosCon2.qdnaseq.bed", + "PosCon2/qdnaseq/PosCon2.qdnaseq_segments.txt", + "PosCon2/qdnaseq/statistics.out", + "PosCon2/wisecondorx/PosCon2.wisecondorx_aberrations.bed", + "PosCon2/wisecondorx/PosCon2.wisecondorx_bins.bed", + "PosCon2/wisecondorx/PosCon2.wisecondorx_segments.bed", + "PosCon2/wisecondorx/PosCon2.wisecondorx_statistics.txt", + "PosCon2/wisecondorx/chr1.png", + "PosCon2/wisecondorx/chr22.png", + "PosCon2/wisecondorx/genome_wide.png", "PosCon3/PosCon3.cnv.vcf.gz", "PosCon3/PosCon3.cnv.vcf.gz.tbi", - "PosCon3/PosCon3.qdnaseq.qdnaseq.bed", - "PosCon3/PosCon3.qdnaseq.qdnaseq_segments.txt", - "PosCon3/PosCon3.qdnaseq.statistics.out", "PosCon3/PosCon3.repeats.vcf.gz", "PosCon3/PosCon3.repeats.vcf.gz.tbi", "PosCon3/PosCon3.sv.vcf.gz", "PosCon3/PosCon3.sv.vcf.gz.tbi", - "PosCon3/PosCon3.wisecondorx.chr1.png", - "PosCon3/PosCon3.wisecondorx.chr22.png", - "PosCon3/PosCon3.wisecondorx.genome_wide.png", - "PosCon3/PosCon3.wisecondorx.wisecondorx_aberrations.bed", - "PosCon3/PosCon3.wisecondorx.wisecondorx_bins.bed", - "PosCon3/PosCon3.wisecondorx.wisecondorx_segments.bed", - "PosCon3/PosCon3.wisecondorx.wisecondorx_statistics.txt", + "PosCon3/qdnaseq/PosCon3.qdnaseq.bed", + "PosCon3/qdnaseq/PosCon3.qdnaseq_segments.txt", + "PosCon3/qdnaseq/statistics.out", + "PosCon3/wisecondorx/PosCon3.wisecondorx_aberrations.bed", + "PosCon3/wisecondorx/PosCon3.wisecondorx_bins.bed", + "PosCon3/wisecondorx/PosCon3.wisecondorx_segments.bed", + "PosCon3/wisecondorx/PosCon3.wisecondorx_statistics.txt", + "PosCon3/wisecondorx/chr1.png", + "PosCon3/wisecondorx/chr22.png", + "PosCon3/wisecondorx/genome_wide.png", "PosCon4/PosCon4.cnv.vcf.gz", "PosCon4/PosCon4.cnv.vcf.gz.tbi", - "PosCon4/PosCon4.qdnaseq.qdnaseq.bed", - "PosCon4/PosCon4.qdnaseq.qdnaseq_segments.txt", - "PosCon4/PosCon4.qdnaseq.statistics.out", "PosCon4/PosCon4.repeats.vcf.gz", "PosCon4/PosCon4.repeats.vcf.gz.tbi", "PosCon4/PosCon4.sv.vcf.gz", "PosCon4/PosCon4.sv.vcf.gz.tbi", - "PosCon4/PosCon4.wisecondorx.chr1.png", - "PosCon4/PosCon4.wisecondorx.chr22.png", - "PosCon4/PosCon4.wisecondorx.genome_wide.png", - "PosCon4/PosCon4.wisecondorx.wisecondorx_aberrations.bed", - "PosCon4/PosCon4.wisecondorx.wisecondorx_bins.bed", - "PosCon4/PosCon4.wisecondorx.wisecondorx_segments.bed", - "PosCon4/PosCon4.wisecondorx.wisecondorx_statistics.txt", + "PosCon4/qdnaseq/PosCon4.qdnaseq.bed", + "PosCon4/qdnaseq/PosCon4.qdnaseq_segments.txt", + "PosCon4/qdnaseq/statistics.out", + "PosCon4/wisecondorx/PosCon4.wisecondorx_aberrations.bed", + "PosCon4/wisecondorx/PosCon4.wisecondorx_bins.bed", + "PosCon4/wisecondorx/PosCon4.wisecondorx_segments.bed", + "PosCon4/wisecondorx/PosCon4.wisecondorx_statistics.txt", + "PosCon4/wisecondorx/chr1.png", + "PosCon4/wisecondorx/chr22.png", + "PosCon4/wisecondorx/genome_wide.png", "multiqc/multiqc_report.html", "samplesheet.csv" ] ], "meta": { - "nf-test": "0.9.1", - "nextflow": "24.10.3" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2025-02-04T14:35:47.691405609" + "timestamp": "2025-07-10T16:18:46.855944925" }, "concat": { "content": [ @@ -85,63 +85,63 @@ ], [ - "PosCon1/PosCon1.qdnaseq.qdnaseq.bed", - "PosCon1/PosCon1.qdnaseq.qdnaseq_segments.txt", - "PosCon1/PosCon1.qdnaseq.statistics.out", "PosCon1/PosCon1.vcf.gz", "PosCon1/PosCon1.vcf.gz.tbi", - "PosCon1/PosCon1.wisecondorx.chr1.png", - "PosCon1/PosCon1.wisecondorx.chr22.png", - "PosCon1/PosCon1.wisecondorx.genome_wide.png", - "PosCon1/PosCon1.wisecondorx.wisecondorx_aberrations.bed", - "PosCon1/PosCon1.wisecondorx.wisecondorx_bins.bed", - "PosCon1/PosCon1.wisecondorx.wisecondorx_segments.bed", - "PosCon1/PosCon1.wisecondorx.wisecondorx_statistics.txt", - "PosCon2/PosCon2.qdnaseq.qdnaseq.bed", - "PosCon2/PosCon2.qdnaseq.qdnaseq_segments.txt", - "PosCon2/PosCon2.qdnaseq.statistics.out", + "PosCon1/qdnaseq/PosCon1.qdnaseq.bed", + "PosCon1/qdnaseq/PosCon1.qdnaseq_segments.txt", + "PosCon1/qdnaseq/statistics.out", + "PosCon1/wisecondorx/PosCon1.wisecondorx_aberrations.bed", + "PosCon1/wisecondorx/PosCon1.wisecondorx_bins.bed", + "PosCon1/wisecondorx/PosCon1.wisecondorx_segments.bed", + "PosCon1/wisecondorx/PosCon1.wisecondorx_statistics.txt", + "PosCon1/wisecondorx/chr1.png", + "PosCon1/wisecondorx/chr22.png", + "PosCon1/wisecondorx/genome_wide.png", "PosCon2/PosCon2.vcf.gz", "PosCon2/PosCon2.vcf.gz.tbi", - "PosCon2/PosCon2.wisecondorx.chr1.png", - "PosCon2/PosCon2.wisecondorx.chr22.png", - "PosCon2/PosCon2.wisecondorx.genome_wide.png", - "PosCon2/PosCon2.wisecondorx.wisecondorx_aberrations.bed", - "PosCon2/PosCon2.wisecondorx.wisecondorx_bins.bed", - "PosCon2/PosCon2.wisecondorx.wisecondorx_segments.bed", - "PosCon2/PosCon2.wisecondorx.wisecondorx_statistics.txt", - "PosCon3/PosCon3.qdnaseq.qdnaseq.bed", - "PosCon3/PosCon3.qdnaseq.qdnaseq_segments.txt", - "PosCon3/PosCon3.qdnaseq.statistics.out", + "PosCon2/qdnaseq/PosCon2.qdnaseq.bed", + "PosCon2/qdnaseq/PosCon2.qdnaseq_segments.txt", + "PosCon2/qdnaseq/statistics.out", + "PosCon2/wisecondorx/PosCon2.wisecondorx_aberrations.bed", + "PosCon2/wisecondorx/PosCon2.wisecondorx_bins.bed", + "PosCon2/wisecondorx/PosCon2.wisecondorx_segments.bed", + "PosCon2/wisecondorx/PosCon2.wisecondorx_statistics.txt", + "PosCon2/wisecondorx/chr1.png", + "PosCon2/wisecondorx/chr22.png", + "PosCon2/wisecondorx/genome_wide.png", "PosCon3/PosCon3.vcf.gz", "PosCon3/PosCon3.vcf.gz.tbi", - "PosCon3/PosCon3.wisecondorx.chr1.png", - "PosCon3/PosCon3.wisecondorx.chr22.png", - "PosCon3/PosCon3.wisecondorx.genome_wide.png", - "PosCon3/PosCon3.wisecondorx.wisecondorx_aberrations.bed", - "PosCon3/PosCon3.wisecondorx.wisecondorx_bins.bed", - "PosCon3/PosCon3.wisecondorx.wisecondorx_segments.bed", - "PosCon3/PosCon3.wisecondorx.wisecondorx_statistics.txt", - "PosCon4/PosCon4.qdnaseq.qdnaseq.bed", - "PosCon4/PosCon4.qdnaseq.qdnaseq_segments.txt", - "PosCon4/PosCon4.qdnaseq.statistics.out", + "PosCon3/qdnaseq/PosCon3.qdnaseq.bed", + "PosCon3/qdnaseq/PosCon3.qdnaseq_segments.txt", + "PosCon3/qdnaseq/statistics.out", + "PosCon3/wisecondorx/PosCon3.wisecondorx_aberrations.bed", + "PosCon3/wisecondorx/PosCon3.wisecondorx_bins.bed", + "PosCon3/wisecondorx/PosCon3.wisecondorx_segments.bed", + "PosCon3/wisecondorx/PosCon3.wisecondorx_statistics.txt", + "PosCon3/wisecondorx/chr1.png", + "PosCon3/wisecondorx/chr22.png", + "PosCon3/wisecondorx/genome_wide.png", "PosCon4/PosCon4.vcf.gz", "PosCon4/PosCon4.vcf.gz.tbi", - "PosCon4/PosCon4.wisecondorx.chr1.png", - "PosCon4/PosCon4.wisecondorx.chr22.png", - "PosCon4/PosCon4.wisecondorx.genome_wide.png", - "PosCon4/PosCon4.wisecondorx.wisecondorx_aberrations.bed", - "PosCon4/PosCon4.wisecondorx.wisecondorx_bins.bed", - "PosCon4/PosCon4.wisecondorx.wisecondorx_segments.bed", - "PosCon4/PosCon4.wisecondorx.wisecondorx_statistics.txt", + "PosCon4/qdnaseq/PosCon4.qdnaseq.bed", + "PosCon4/qdnaseq/PosCon4.qdnaseq_segments.txt", + "PosCon4/qdnaseq/statistics.out", + "PosCon4/wisecondorx/PosCon4.wisecondorx_aberrations.bed", + "PosCon4/wisecondorx/PosCon4.wisecondorx_bins.bed", + "PosCon4/wisecondorx/PosCon4.wisecondorx_segments.bed", + "PosCon4/wisecondorx/PosCon4.wisecondorx_statistics.txt", + "PosCon4/wisecondorx/chr1.png", + "PosCon4/wisecondorx/chr22.png", + "PosCon4/wisecondorx/genome_wide.png", "multiqc/multiqc_report.html", "samplesheet.csv" ] ], "meta": { - "nf-test": "0.9.1", - "nextflow": "24.10.3" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2025-02-04T14:37:23.059367032" + "timestamp": "2025-07-10T16:20:18.015157817" }, "output callers": { "content": [ @@ -151,108 +151,108 @@ [ "PosCon1/PosCon1.cnv.vcf.gz", "PosCon1/PosCon1.cnv.vcf.gz.tbi", - "PosCon1/PosCon1.qdnaseq.qdnaseq.bed", - "PosCon1/PosCon1.qdnaseq.qdnaseq_segments.txt", - "PosCon1/PosCon1.qdnaseq.statistics.out", "PosCon1/PosCon1.repeats.vcf.gz", "PosCon1/PosCon1.repeats.vcf.gz.tbi", "PosCon1/PosCon1.sv.vcf.gz", "PosCon1/PosCon1.sv.vcf.gz.tbi", - "PosCon1/PosCon1.wisecondorx.chr1.png", - "PosCon1/PosCon1.wisecondorx.chr22.png", - "PosCon1/PosCon1.wisecondorx.genome_wide.png", - "PosCon1/PosCon1.wisecondorx.wisecondorx_aberrations.bed", - "PosCon1/PosCon1.wisecondorx.wisecondorx_bins.bed", - "PosCon1/PosCon1.wisecondorx.wisecondorx_segments.bed", - "PosCon1/PosCon1.wisecondorx.wisecondorx_statistics.txt", "PosCon1/delly/PosCon1.vcf.gz", "PosCon1/delly/PosCon1.vcf.gz.tbi", "PosCon1/expansionhunter/PosCon1.vcf.gz", "PosCon1/expansionhunter/PosCon1.vcf.gz.tbi", "PosCon1/manta/PosCon1.vcf.gz", "PosCon1/manta/PosCon1.vcf.gz.tbi", + "PosCon1/qdnaseq/PosCon1.qdnaseq.bed", + "PosCon1/qdnaseq/PosCon1.qdnaseq_segments.txt", + "PosCon1/qdnaseq/statistics.out", "PosCon1/smoove/PosCon1.vcf.gz", "PosCon1/smoove/PosCon1.vcf.gz.tbi", + "PosCon1/wisecondorx/PosCon1.wisecondorx_aberrations.bed", + "PosCon1/wisecondorx/PosCon1.wisecondorx_bins.bed", + "PosCon1/wisecondorx/PosCon1.wisecondorx_segments.bed", + "PosCon1/wisecondorx/PosCon1.wisecondorx_statistics.txt", + "PosCon1/wisecondorx/chr1.png", + "PosCon1/wisecondorx/chr22.png", + "PosCon1/wisecondorx/genome_wide.png", "PosCon2/PosCon2.cnv.vcf.gz", "PosCon2/PosCon2.cnv.vcf.gz.tbi", - "PosCon2/PosCon2.qdnaseq.qdnaseq.bed", - "PosCon2/PosCon2.qdnaseq.qdnaseq_segments.txt", - "PosCon2/PosCon2.qdnaseq.statistics.out", "PosCon2/PosCon2.repeats.vcf.gz", "PosCon2/PosCon2.repeats.vcf.gz.tbi", "PosCon2/PosCon2.sv.vcf.gz", "PosCon2/PosCon2.sv.vcf.gz.tbi", - "PosCon2/PosCon2.wisecondorx.chr1.png", - "PosCon2/PosCon2.wisecondorx.chr22.png", - "PosCon2/PosCon2.wisecondorx.genome_wide.png", - "PosCon2/PosCon2.wisecondorx.wisecondorx_aberrations.bed", - "PosCon2/PosCon2.wisecondorx.wisecondorx_bins.bed", - "PosCon2/PosCon2.wisecondorx.wisecondorx_segments.bed", - "PosCon2/PosCon2.wisecondorx.wisecondorx_statistics.txt", "PosCon2/delly/PosCon2.vcf.gz", "PosCon2/delly/PosCon2.vcf.gz.tbi", "PosCon2/expansionhunter/PosCon2.vcf.gz", "PosCon2/expansionhunter/PosCon2.vcf.gz.tbi", "PosCon2/manta/PosCon2.vcf.gz", "PosCon2/manta/PosCon2.vcf.gz.tbi", + "PosCon2/qdnaseq/PosCon2.qdnaseq.bed", + "PosCon2/qdnaseq/PosCon2.qdnaseq_segments.txt", + "PosCon2/qdnaseq/statistics.out", "PosCon2/smoove/PosCon2.vcf.gz", "PosCon2/smoove/PosCon2.vcf.gz.tbi", + "PosCon2/wisecondorx/PosCon2.wisecondorx_aberrations.bed", + "PosCon2/wisecondorx/PosCon2.wisecondorx_bins.bed", + "PosCon2/wisecondorx/PosCon2.wisecondorx_segments.bed", + "PosCon2/wisecondorx/PosCon2.wisecondorx_statistics.txt", + "PosCon2/wisecondorx/chr1.png", + "PosCon2/wisecondorx/chr22.png", + "PosCon2/wisecondorx/genome_wide.png", "PosCon3/PosCon3.cnv.vcf.gz", "PosCon3/PosCon3.cnv.vcf.gz.tbi", - "PosCon3/PosCon3.qdnaseq.qdnaseq.bed", - "PosCon3/PosCon3.qdnaseq.qdnaseq_segments.txt", - "PosCon3/PosCon3.qdnaseq.statistics.out", "PosCon3/PosCon3.repeats.vcf.gz", "PosCon3/PosCon3.repeats.vcf.gz.tbi", "PosCon3/PosCon3.sv.vcf.gz", "PosCon3/PosCon3.sv.vcf.gz.tbi", - "PosCon3/PosCon3.wisecondorx.chr1.png", - "PosCon3/PosCon3.wisecondorx.chr22.png", - "PosCon3/PosCon3.wisecondorx.genome_wide.png", - "PosCon3/PosCon3.wisecondorx.wisecondorx_aberrations.bed", - "PosCon3/PosCon3.wisecondorx.wisecondorx_bins.bed", - "PosCon3/PosCon3.wisecondorx.wisecondorx_segments.bed", - "PosCon3/PosCon3.wisecondorx.wisecondorx_statistics.txt", "PosCon3/delly/PosCon3.vcf.gz", "PosCon3/delly/PosCon3.vcf.gz.tbi", "PosCon3/expansionhunter/PosCon3.vcf.gz", "PosCon3/expansionhunter/PosCon3.vcf.gz.tbi", "PosCon3/manta/PosCon3.vcf.gz", "PosCon3/manta/PosCon3.vcf.gz.tbi", + "PosCon3/qdnaseq/PosCon3.qdnaseq.bed", + "PosCon3/qdnaseq/PosCon3.qdnaseq_segments.txt", + "PosCon3/qdnaseq/statistics.out", "PosCon3/smoove/PosCon3.vcf.gz", "PosCon3/smoove/PosCon3.vcf.gz.tbi", + "PosCon3/wisecondorx/PosCon3.wisecondorx_aberrations.bed", + "PosCon3/wisecondorx/PosCon3.wisecondorx_bins.bed", + "PosCon3/wisecondorx/PosCon3.wisecondorx_segments.bed", + "PosCon3/wisecondorx/PosCon3.wisecondorx_statistics.txt", + "PosCon3/wisecondorx/chr1.png", + "PosCon3/wisecondorx/chr22.png", + "PosCon3/wisecondorx/genome_wide.png", "PosCon4/PosCon4.cnv.vcf.gz", "PosCon4/PosCon4.cnv.vcf.gz.tbi", - "PosCon4/PosCon4.qdnaseq.qdnaseq.bed", - "PosCon4/PosCon4.qdnaseq.qdnaseq_segments.txt", - "PosCon4/PosCon4.qdnaseq.statistics.out", "PosCon4/PosCon4.repeats.vcf.gz", "PosCon4/PosCon4.repeats.vcf.gz.tbi", "PosCon4/PosCon4.sv.vcf.gz", "PosCon4/PosCon4.sv.vcf.gz.tbi", - "PosCon4/PosCon4.wisecondorx.chr1.png", - "PosCon4/PosCon4.wisecondorx.chr22.png", - "PosCon4/PosCon4.wisecondorx.genome_wide.png", - "PosCon4/PosCon4.wisecondorx.wisecondorx_aberrations.bed", - "PosCon4/PosCon4.wisecondorx.wisecondorx_bins.bed", - "PosCon4/PosCon4.wisecondorx.wisecondorx_segments.bed", - "PosCon4/PosCon4.wisecondorx.wisecondorx_statistics.txt", "PosCon4/delly/PosCon4.vcf.gz", "PosCon4/delly/PosCon4.vcf.gz.tbi", "PosCon4/expansionhunter/PosCon4.vcf.gz", "PosCon4/expansionhunter/PosCon4.vcf.gz.tbi", "PosCon4/manta/PosCon4.vcf.gz", "PosCon4/manta/PosCon4.vcf.gz.tbi", + "PosCon4/qdnaseq/PosCon4.qdnaseq.bed", + "PosCon4/qdnaseq/PosCon4.qdnaseq_segments.txt", + "PosCon4/qdnaseq/statistics.out", "PosCon4/smoove/PosCon4.vcf.gz", "PosCon4/smoove/PosCon4.vcf.gz.tbi", + "PosCon4/wisecondorx/PosCon4.wisecondorx_aberrations.bed", + "PosCon4/wisecondorx/PosCon4.wisecondorx_bins.bed", + "PosCon4/wisecondorx/PosCon4.wisecondorx_segments.bed", + "PosCon4/wisecondorx/PosCon4.wisecondorx_statistics.txt", + "PosCon4/wisecondorx/chr1.png", + "PosCon4/wisecondorx/chr22.png", + "PosCon4/wisecondorx/genome_wide.png", "multiqc/multiqc_report.html", "samplesheet.csv" ] ], "meta": { - "nf-test": "0.9.1", - "nextflow": "24.10.3" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2025-02-04T14:43:02.361185058" + "timestamp": "2025-07-10T16:21:41.411733092" } } \ No newline at end of file diff --git a/tests/pipeline/cnv/cnv.nf.test.snap b/tests/pipeline/cnv/cnv.nf.test.snap index 4210435a..697e770c 100644 --- a/tests/pipeline/cnv/cnv.nf.test.snap +++ b/tests/pipeline/cnv/cnv.nf.test.snap @@ -7,61 +7,61 @@ [ "PosCon1/PosCon1.cnv.vcf.gz", "PosCon1/PosCon1.cnv.vcf.gz.tbi", - "PosCon1/PosCon1.qdnaseq.qdnaseq.bed", - "PosCon1/PosCon1.qdnaseq.qdnaseq_segments.txt", - "PosCon1/PosCon1.qdnaseq.statistics.out", - "PosCon1/PosCon1.wisecondorx.chr1.png", - "PosCon1/PosCon1.wisecondorx.chr22.png", - "PosCon1/PosCon1.wisecondorx.genome_wide.png", - "PosCon1/PosCon1.wisecondorx.wisecondorx_aberrations.bed", - "PosCon1/PosCon1.wisecondorx.wisecondorx_bins.bed", - "PosCon1/PosCon1.wisecondorx.wisecondorx_segments.bed", - "PosCon1/PosCon1.wisecondorx.wisecondorx_statistics.txt", + "PosCon1/qdnaseq/PosCon1.qdnaseq.bed", + "PosCon1/qdnaseq/PosCon1.qdnaseq_segments.txt", + "PosCon1/qdnaseq/statistics.out", + "PosCon1/wisecondorx/PosCon1.wisecondorx_aberrations.bed", + "PosCon1/wisecondorx/PosCon1.wisecondorx_bins.bed", + "PosCon1/wisecondorx/PosCon1.wisecondorx_segments.bed", + "PosCon1/wisecondorx/PosCon1.wisecondorx_statistics.txt", + "PosCon1/wisecondorx/chr1.png", + "PosCon1/wisecondorx/chr22.png", + "PosCon1/wisecondorx/genome_wide.png", "PosCon2/PosCon2.cnv.vcf.gz", "PosCon2/PosCon2.cnv.vcf.gz.tbi", - "PosCon2/PosCon2.qdnaseq.qdnaseq.bed", - "PosCon2/PosCon2.qdnaseq.qdnaseq_segments.txt", - "PosCon2/PosCon2.qdnaseq.statistics.out", - "PosCon2/PosCon2.wisecondorx.chr1.png", - "PosCon2/PosCon2.wisecondorx.chr22.png", - "PosCon2/PosCon2.wisecondorx.genome_wide.png", - "PosCon2/PosCon2.wisecondorx.wisecondorx_aberrations.bed", - "PosCon2/PosCon2.wisecondorx.wisecondorx_bins.bed", - "PosCon2/PosCon2.wisecondorx.wisecondorx_segments.bed", - "PosCon2/PosCon2.wisecondorx.wisecondorx_statistics.txt", + "PosCon2/qdnaseq/PosCon2.qdnaseq.bed", + "PosCon2/qdnaseq/PosCon2.qdnaseq_segments.txt", + "PosCon2/qdnaseq/statistics.out", + "PosCon2/wisecondorx/PosCon2.wisecondorx_aberrations.bed", + "PosCon2/wisecondorx/PosCon2.wisecondorx_bins.bed", + "PosCon2/wisecondorx/PosCon2.wisecondorx_segments.bed", + "PosCon2/wisecondorx/PosCon2.wisecondorx_statistics.txt", + "PosCon2/wisecondorx/chr1.png", + "PosCon2/wisecondorx/chr22.png", + "PosCon2/wisecondorx/genome_wide.png", "PosCon3/PosCon3.cnv.vcf.gz", "PosCon3/PosCon3.cnv.vcf.gz.tbi", - "PosCon3/PosCon3.qdnaseq.qdnaseq.bed", - "PosCon3/PosCon3.qdnaseq.qdnaseq_segments.txt", - "PosCon3/PosCon3.qdnaseq.statistics.out", - "PosCon3/PosCon3.wisecondorx.chr1.png", - "PosCon3/PosCon3.wisecondorx.chr22.png", - "PosCon3/PosCon3.wisecondorx.genome_wide.png", - "PosCon3/PosCon3.wisecondorx.wisecondorx_aberrations.bed", - "PosCon3/PosCon3.wisecondorx.wisecondorx_bins.bed", - "PosCon3/PosCon3.wisecondorx.wisecondorx_segments.bed", - "PosCon3/PosCon3.wisecondorx.wisecondorx_statistics.txt", + "PosCon3/qdnaseq/PosCon3.qdnaseq.bed", + "PosCon3/qdnaseq/PosCon3.qdnaseq_segments.txt", + "PosCon3/qdnaseq/statistics.out", + "PosCon3/wisecondorx/PosCon3.wisecondorx_aberrations.bed", + "PosCon3/wisecondorx/PosCon3.wisecondorx_bins.bed", + "PosCon3/wisecondorx/PosCon3.wisecondorx_segments.bed", + "PosCon3/wisecondorx/PosCon3.wisecondorx_statistics.txt", + "PosCon3/wisecondorx/chr1.png", + "PosCon3/wisecondorx/chr22.png", + "PosCon3/wisecondorx/genome_wide.png", "PosCon4/PosCon4.cnv.vcf.gz", "PosCon4/PosCon4.cnv.vcf.gz.tbi", - "PosCon4/PosCon4.qdnaseq.qdnaseq.bed", - "PosCon4/PosCon4.qdnaseq.qdnaseq_segments.txt", - "PosCon4/PosCon4.qdnaseq.statistics.out", - "PosCon4/PosCon4.wisecondorx.chr1.png", - "PosCon4/PosCon4.wisecondorx.chr22.png", - "PosCon4/PosCon4.wisecondorx.genome_wide.png", - "PosCon4/PosCon4.wisecondorx.wisecondorx_aberrations.bed", - "PosCon4/PosCon4.wisecondorx.wisecondorx_bins.bed", - "PosCon4/PosCon4.wisecondorx.wisecondorx_segments.bed", - "PosCon4/PosCon4.wisecondorx.wisecondorx_statistics.txt", + "PosCon4/qdnaseq/PosCon4.qdnaseq.bed", + "PosCon4/qdnaseq/PosCon4.qdnaseq_segments.txt", + "PosCon4/qdnaseq/statistics.out", + "PosCon4/wisecondorx/PosCon4.wisecondorx_aberrations.bed", + "PosCon4/wisecondorx/PosCon4.wisecondorx_bins.bed", + "PosCon4/wisecondorx/PosCon4.wisecondorx_segments.bed", + "PosCon4/wisecondorx/PosCon4.wisecondorx_statistics.txt", + "PosCon4/wisecondorx/chr1.png", + "PosCon4/wisecondorx/chr22.png", + "PosCon4/wisecondorx/genome_wide.png", "multiqc/multiqc_report.html", "samplesheet.csv" ] ], "meta": { - "nf-test": "0.9.1", - "nextflow": "24.10.3" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2025-02-04T14:44:41.409129649" + "timestamp": "2025-07-10T16:24:38.383599515" }, "qdnaseq": { "content": [ @@ -71,32 +71,32 @@ [ "PosCon1/PosCon1.cnv.vcf.gz", "PosCon1/PosCon1.cnv.vcf.gz.tbi", - "PosCon1/PosCon1.qdnaseq.qdnaseq.bed", - "PosCon1/PosCon1.qdnaseq.qdnaseq_segments.txt", - "PosCon1/PosCon1.qdnaseq.statistics.out", + "PosCon1/qdnaseq/PosCon1.qdnaseq.bed", + "PosCon1/qdnaseq/PosCon1.qdnaseq_segments.txt", + "PosCon1/qdnaseq/statistics.out", "PosCon2/PosCon2.cnv.vcf.gz", "PosCon2/PosCon2.cnv.vcf.gz.tbi", - "PosCon2/PosCon2.qdnaseq.qdnaseq.bed", - "PosCon2/PosCon2.qdnaseq.qdnaseq_segments.txt", - "PosCon2/PosCon2.qdnaseq.statistics.out", + "PosCon2/qdnaseq/PosCon2.qdnaseq.bed", + "PosCon2/qdnaseq/PosCon2.qdnaseq_segments.txt", + "PosCon2/qdnaseq/statistics.out", "PosCon3/PosCon3.cnv.vcf.gz", "PosCon3/PosCon3.cnv.vcf.gz.tbi", - "PosCon3/PosCon3.qdnaseq.qdnaseq.bed", - "PosCon3/PosCon3.qdnaseq.qdnaseq_segments.txt", - "PosCon3/PosCon3.qdnaseq.statistics.out", + "PosCon3/qdnaseq/PosCon3.qdnaseq.bed", + "PosCon3/qdnaseq/PosCon3.qdnaseq_segments.txt", + "PosCon3/qdnaseq/statistics.out", "PosCon4/PosCon4.cnv.vcf.gz", "PosCon4/PosCon4.cnv.vcf.gz.tbi", - "PosCon4/PosCon4.qdnaseq.qdnaseq.bed", - "PosCon4/PosCon4.qdnaseq.qdnaseq_segments.txt", - "PosCon4/PosCon4.qdnaseq.statistics.out", + "PosCon4/qdnaseq/PosCon4.qdnaseq.bed", + "PosCon4/qdnaseq/PosCon4.qdnaseq_segments.txt", + "PosCon4/qdnaseq/statistics.out", "multiqc/multiqc_report.html", "samplesheet.csv" ] ], "meta": { - "nf-test": "0.9.1", - "nextflow": "24.10.3" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2025-02-04T14:43:48.170539881" + "timestamp": "2025-07-10T16:23:49.236370694" } } \ No newline at end of file diff --git a/tests/pipeline/duplicates/duplicates.nf.test.snap b/tests/pipeline/duplicates/duplicates.nf.test.snap index f866eba8..0d3a86f2 100644 --- a/tests/pipeline/duplicates/duplicates.nf.test.snap +++ b/tests/pipeline/duplicates/duplicates.nf.test.snap @@ -11,34 +11,34 @@ "PosCon1/PosCon1.repeats.vcf.gz.tbi", "PosCon1/PosCon1.sv.vcf.gz", "PosCon1/PosCon1.sv.vcf.gz.tbi", - "PosCon1/PosCon1.wisecondorx.chr1.png", - "PosCon1/PosCon1.wisecondorx.chr22.png", - "PosCon1/PosCon1.wisecondorx.genome_wide.png", - "PosCon1/PosCon1.wisecondorx.wisecondorx_aberrations.bed", - "PosCon1/PosCon1.wisecondorx.wisecondorx_bins.bed", - "PosCon1/PosCon1.wisecondorx.wisecondorx_segments.bed", - "PosCon1/PosCon1.wisecondorx.wisecondorx_statistics.txt", + "PosCon1/wisecondorx/PosCon1.wisecondorx_aberrations.bed", + "PosCon1/wisecondorx/PosCon1.wisecondorx_bins.bed", + "PosCon1/wisecondorx/PosCon1.wisecondorx_segments.bed", + "PosCon1/wisecondorx/PosCon1.wisecondorx_statistics.txt", + "PosCon1/wisecondorx/chr1.png", + "PosCon1/wisecondorx/chr22.png", + "PosCon1/wisecondorx/genome_wide.png", "PosCon3/PosCon3.cnv.vcf.gz", "PosCon3/PosCon3.cnv.vcf.gz.tbi", "PosCon3/PosCon3.repeats.vcf.gz", "PosCon3/PosCon3.repeats.vcf.gz.tbi", "PosCon3/PosCon3.sv.vcf.gz", "PosCon3/PosCon3.sv.vcf.gz.tbi", - "PosCon3/PosCon3.wisecondorx.chr1.png", - "PosCon3/PosCon3.wisecondorx.chr22.png", - "PosCon3/PosCon3.wisecondorx.genome_wide.png", - "PosCon3/PosCon3.wisecondorx.wisecondorx_aberrations.bed", - "PosCon3/PosCon3.wisecondorx.wisecondorx_bins.bed", - "PosCon3/PosCon3.wisecondorx.wisecondorx_segments.bed", - "PosCon3/PosCon3.wisecondorx.wisecondorx_statistics.txt", + "PosCon3/wisecondorx/PosCon3.wisecondorx_aberrations.bed", + "PosCon3/wisecondorx/PosCon3.wisecondorx_bins.bed", + "PosCon3/wisecondorx/PosCon3.wisecondorx_segments.bed", + "PosCon3/wisecondorx/PosCon3.wisecondorx_statistics.txt", + "PosCon3/wisecondorx/chr1.png", + "PosCon3/wisecondorx/chr22.png", + "PosCon3/wisecondorx/genome_wide.png", "multiqc/multiqc_report.html", "samplesheet.csv" ] ], "meta": { - "nf-test": "0.9.1", - "nextflow": "24.10.3" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2025-02-04T14:45:29.439885168" + "timestamp": "2025-07-10T16:25:25.233371377" } } \ No newline at end of file diff --git a/tests/pipeline/families/families.nf.test.snap b/tests/pipeline/families/families.nf.test.snap index a8afdaee..1946cf58 100644 --- a/tests/pipeline/families/families.nf.test.snap +++ b/tests/pipeline/families/families.nf.test.snap @@ -5,42 +5,42 @@ ], [ - "PosCon1/PosCon1.qdnaseq.qdnaseq.bed", - "PosCon1/PosCon1.qdnaseq.qdnaseq_segments.txt", - "PosCon1/PosCon1.qdnaseq.statistics.out", "PosCon1/PosCon1.vcf.gz", "PosCon1/PosCon1.vcf.gz.tbi", - "PosCon1/PosCon1.wisecondorx.chr1.png", - "PosCon1/PosCon1.wisecondorx.chr22.png", - "PosCon1/PosCon1.wisecondorx.genome_wide.png", - "PosCon1/PosCon1.wisecondorx.wisecondorx_aberrations.bed", - "PosCon1/PosCon1.wisecondorx.wisecondorx_bins.bed", - "PosCon1/PosCon1.wisecondorx.wisecondorx_segments.bed", - "PosCon1/PosCon1.wisecondorx.wisecondorx_statistics.txt", - "PosCon2/PosCon2.qdnaseq.qdnaseq.bed", - "PosCon2/PosCon2.qdnaseq.qdnaseq_segments.txt", - "PosCon2/PosCon2.qdnaseq.statistics.out", + "PosCon1/qdnaseq/PosCon1.qdnaseq.bed", + "PosCon1/qdnaseq/PosCon1.qdnaseq_segments.txt", + "PosCon1/qdnaseq/statistics.out", + "PosCon1/wisecondorx/PosCon1.wisecondorx_aberrations.bed", + "PosCon1/wisecondorx/PosCon1.wisecondorx_bins.bed", + "PosCon1/wisecondorx/PosCon1.wisecondorx_segments.bed", + "PosCon1/wisecondorx/PosCon1.wisecondorx_statistics.txt", + "PosCon1/wisecondorx/chr1.png", + "PosCon1/wisecondorx/chr22.png", + "PosCon1/wisecondorx/genome_wide.png", "PosCon2/PosCon2.vcf.gz", "PosCon2/PosCon2.vcf.gz.tbi", - "PosCon2/PosCon2.wisecondorx.chr1.png", - "PosCon2/PosCon2.wisecondorx.chr22.png", - "PosCon2/PosCon2.wisecondorx.genome_wide.png", - "PosCon2/PosCon2.wisecondorx.wisecondorx_aberrations.bed", - "PosCon2/PosCon2.wisecondorx.wisecondorx_bins.bed", - "PosCon2/PosCon2.wisecondorx.wisecondorx_segments.bed", - "PosCon2/PosCon2.wisecondorx.wisecondorx_statistics.txt", - "PosCon3/PosCon3.qdnaseq.qdnaseq.bed", - "PosCon3/PosCon3.qdnaseq.qdnaseq_segments.txt", - "PosCon3/PosCon3.qdnaseq.statistics.out", + "PosCon2/qdnaseq/PosCon2.qdnaseq.bed", + "PosCon2/qdnaseq/PosCon2.qdnaseq_segments.txt", + "PosCon2/qdnaseq/statistics.out", + "PosCon2/wisecondorx/PosCon2.wisecondorx_aberrations.bed", + "PosCon2/wisecondorx/PosCon2.wisecondorx_bins.bed", + "PosCon2/wisecondorx/PosCon2.wisecondorx_segments.bed", + "PosCon2/wisecondorx/PosCon2.wisecondorx_statistics.txt", + "PosCon2/wisecondorx/chr1.png", + "PosCon2/wisecondorx/chr22.png", + "PosCon2/wisecondorx/genome_wide.png", "PosCon3/PosCon3.vcf.gz", "PosCon3/PosCon3.vcf.gz.tbi", - "PosCon3/PosCon3.wisecondorx.chr1.png", - "PosCon3/PosCon3.wisecondorx.chr22.png", - "PosCon3/PosCon3.wisecondorx.genome_wide.png", - "PosCon3/PosCon3.wisecondorx.wisecondorx_aberrations.bed", - "PosCon3/PosCon3.wisecondorx.wisecondorx_bins.bed", - "PosCon3/PosCon3.wisecondorx.wisecondorx_segments.bed", - "PosCon3/PosCon3.wisecondorx.wisecondorx_statistics.txt", + "PosCon3/qdnaseq/PosCon3.qdnaseq.bed", + "PosCon3/qdnaseq/PosCon3.qdnaseq_segments.txt", + "PosCon3/qdnaseq/statistics.out", + "PosCon3/wisecondorx/PosCon3.wisecondorx_aberrations.bed", + "PosCon3/wisecondorx/PosCon3.wisecondorx_bins.bed", + "PosCon3/wisecondorx/PosCon3.wisecondorx_segments.bed", + "PosCon3/wisecondorx/PosCon3.wisecondorx_statistics.txt", + "PosCon3/wisecondorx/chr1.png", + "PosCon3/wisecondorx/chr22.png", + "PosCon3/wisecondorx/genome_wide.png", "multiqc/multiqc_report.html", "samplesheet.csv", "test_family/test_family.vcf.gz", @@ -48,10 +48,10 @@ ] ], "meta": { - "nf-test": "0.9.1", - "nextflow": "24.10.3" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2025-02-04T14:58:50.512238846" + "timestamp": "2025-07-10T16:30:04.977643016" }, "family with 2 samples + 1 sample - no concat": { "content": [ @@ -61,52 +61,52 @@ [ "PosCon1/PosCon1.cnv.vcf.gz", "PosCon1/PosCon1.cnv.vcf.gz.tbi", - "PosCon1/PosCon1.qdnaseq.qdnaseq.bed", - "PosCon1/PosCon1.qdnaseq.qdnaseq_segments.txt", - "PosCon1/PosCon1.qdnaseq.statistics.out", "PosCon1/PosCon1.repeats.vcf.gz", "PosCon1/PosCon1.repeats.vcf.gz.tbi", "PosCon1/PosCon1.sv.vcf.gz", "PosCon1/PosCon1.sv.vcf.gz.tbi", - "PosCon1/PosCon1.wisecondorx.chr1.png", - "PosCon1/PosCon1.wisecondorx.chr22.png", - "PosCon1/PosCon1.wisecondorx.genome_wide.png", - "PosCon1/PosCon1.wisecondorx.wisecondorx_aberrations.bed", - "PosCon1/PosCon1.wisecondorx.wisecondorx_bins.bed", - "PosCon1/PosCon1.wisecondorx.wisecondorx_segments.bed", - "PosCon1/PosCon1.wisecondorx.wisecondorx_statistics.txt", + "PosCon1/qdnaseq/PosCon1.qdnaseq.bed", + "PosCon1/qdnaseq/PosCon1.qdnaseq_segments.txt", + "PosCon1/qdnaseq/statistics.out", + "PosCon1/wisecondorx/PosCon1.wisecondorx_aberrations.bed", + "PosCon1/wisecondorx/PosCon1.wisecondorx_bins.bed", + "PosCon1/wisecondorx/PosCon1.wisecondorx_segments.bed", + "PosCon1/wisecondorx/PosCon1.wisecondorx_statistics.txt", + "PosCon1/wisecondorx/chr1.png", + "PosCon1/wisecondorx/chr22.png", + "PosCon1/wisecondorx/genome_wide.png", "PosCon2/PosCon2.cnv.vcf.gz", "PosCon2/PosCon2.cnv.vcf.gz.tbi", - "PosCon2/PosCon2.qdnaseq.qdnaseq.bed", - "PosCon2/PosCon2.qdnaseq.qdnaseq_segments.txt", - "PosCon2/PosCon2.qdnaseq.statistics.out", "PosCon2/PosCon2.repeats.vcf.gz", "PosCon2/PosCon2.repeats.vcf.gz.tbi", "PosCon2/PosCon2.sv.vcf.gz", "PosCon2/PosCon2.sv.vcf.gz.tbi", - "PosCon2/PosCon2.wisecondorx.chr1.png", - "PosCon2/PosCon2.wisecondorx.chr22.png", - "PosCon2/PosCon2.wisecondorx.genome_wide.png", - "PosCon2/PosCon2.wisecondorx.wisecondorx_aberrations.bed", - "PosCon2/PosCon2.wisecondorx.wisecondorx_bins.bed", - "PosCon2/PosCon2.wisecondorx.wisecondorx_segments.bed", - "PosCon2/PosCon2.wisecondorx.wisecondorx_statistics.txt", + "PosCon2/qdnaseq/PosCon2.qdnaseq.bed", + "PosCon2/qdnaseq/PosCon2.qdnaseq_segments.txt", + "PosCon2/qdnaseq/statistics.out", + "PosCon2/wisecondorx/PosCon2.wisecondorx_aberrations.bed", + "PosCon2/wisecondorx/PosCon2.wisecondorx_bins.bed", + "PosCon2/wisecondorx/PosCon2.wisecondorx_segments.bed", + "PosCon2/wisecondorx/PosCon2.wisecondorx_statistics.txt", + "PosCon2/wisecondorx/chr1.png", + "PosCon2/wisecondorx/chr22.png", + "PosCon2/wisecondorx/genome_wide.png", "PosCon3/PosCon3.cnv.vcf.gz", "PosCon3/PosCon3.cnv.vcf.gz.tbi", - "PosCon3/PosCon3.qdnaseq.qdnaseq.bed", - "PosCon3/PosCon3.qdnaseq.qdnaseq_segments.txt", - "PosCon3/PosCon3.qdnaseq.statistics.out", "PosCon3/PosCon3.repeats.vcf.gz", "PosCon3/PosCon3.repeats.vcf.gz.tbi", "PosCon3/PosCon3.sv.vcf.gz", "PosCon3/PosCon3.sv.vcf.gz.tbi", - "PosCon3/PosCon3.wisecondorx.chr1.png", - "PosCon3/PosCon3.wisecondorx.chr22.png", - "PosCon3/PosCon3.wisecondorx.genome_wide.png", - "PosCon3/PosCon3.wisecondorx.wisecondorx_aberrations.bed", - "PosCon3/PosCon3.wisecondorx.wisecondorx_bins.bed", - "PosCon3/PosCon3.wisecondorx.wisecondorx_segments.bed", - "PosCon3/PosCon3.wisecondorx.wisecondorx_statistics.txt", + "PosCon3/qdnaseq/PosCon3.qdnaseq.bed", + "PosCon3/qdnaseq/PosCon3.qdnaseq_segments.txt", + "PosCon3/qdnaseq/statistics.out", + "PosCon3/wisecondorx/PosCon3.wisecondorx_aberrations.bed", + "PosCon3/wisecondorx/PosCon3.wisecondorx_bins.bed", + "PosCon3/wisecondorx/PosCon3.wisecondorx_segments.bed", + "PosCon3/wisecondorx/PosCon3.wisecondorx_statistics.txt", + "PosCon3/wisecondorx/chr1.png", + "PosCon3/wisecondorx/chr22.png", + "PosCon3/wisecondorx/genome_wide.png", "multiqc/multiqc_report.html", "samplesheet.csv", "test_family/test_family.cnv.vcf.gz", @@ -118,10 +118,10 @@ ] ], "meta": { - "nf-test": "0.9.1", - "nextflow": "24.10.3" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2025-02-04T14:49:38.757546959" + "timestamp": "2025-07-10T16:28:52.577447925" }, "family with 3 samples - no concat": { "content": [ @@ -131,52 +131,52 @@ [ "PosCon1/PosCon1.cnv.vcf.gz", "PosCon1/PosCon1.cnv.vcf.gz.tbi", - "PosCon1/PosCon1.qdnaseq.qdnaseq.bed", - "PosCon1/PosCon1.qdnaseq.qdnaseq_segments.txt", - "PosCon1/PosCon1.qdnaseq.statistics.out", "PosCon1/PosCon1.repeats.vcf.gz", "PosCon1/PosCon1.repeats.vcf.gz.tbi", "PosCon1/PosCon1.sv.vcf.gz", "PosCon1/PosCon1.sv.vcf.gz.tbi", - "PosCon1/PosCon1.wisecondorx.chr1.png", - "PosCon1/PosCon1.wisecondorx.chr22.png", - "PosCon1/PosCon1.wisecondorx.genome_wide.png", - "PosCon1/PosCon1.wisecondorx.wisecondorx_aberrations.bed", - "PosCon1/PosCon1.wisecondorx.wisecondorx_bins.bed", - "PosCon1/PosCon1.wisecondorx.wisecondorx_segments.bed", - "PosCon1/PosCon1.wisecondorx.wisecondorx_statistics.txt", + "PosCon1/qdnaseq/PosCon1.qdnaseq.bed", + "PosCon1/qdnaseq/PosCon1.qdnaseq_segments.txt", + "PosCon1/qdnaseq/statistics.out", + "PosCon1/wisecondorx/PosCon1.wisecondorx_aberrations.bed", + "PosCon1/wisecondorx/PosCon1.wisecondorx_bins.bed", + "PosCon1/wisecondorx/PosCon1.wisecondorx_segments.bed", + "PosCon1/wisecondorx/PosCon1.wisecondorx_statistics.txt", + "PosCon1/wisecondorx/chr1.png", + "PosCon1/wisecondorx/chr22.png", + "PosCon1/wisecondorx/genome_wide.png", "PosCon2/PosCon2.cnv.vcf.gz", "PosCon2/PosCon2.cnv.vcf.gz.tbi", - "PosCon2/PosCon2.qdnaseq.qdnaseq.bed", - "PosCon2/PosCon2.qdnaseq.qdnaseq_segments.txt", - "PosCon2/PosCon2.qdnaseq.statistics.out", "PosCon2/PosCon2.repeats.vcf.gz", "PosCon2/PosCon2.repeats.vcf.gz.tbi", "PosCon2/PosCon2.sv.vcf.gz", "PosCon2/PosCon2.sv.vcf.gz.tbi", - "PosCon2/PosCon2.wisecondorx.chr1.png", - "PosCon2/PosCon2.wisecondorx.chr22.png", - "PosCon2/PosCon2.wisecondorx.genome_wide.png", - "PosCon2/PosCon2.wisecondorx.wisecondorx_aberrations.bed", - "PosCon2/PosCon2.wisecondorx.wisecondorx_bins.bed", - "PosCon2/PosCon2.wisecondorx.wisecondorx_segments.bed", - "PosCon2/PosCon2.wisecondorx.wisecondorx_statistics.txt", + "PosCon2/qdnaseq/PosCon2.qdnaseq.bed", + "PosCon2/qdnaseq/PosCon2.qdnaseq_segments.txt", + "PosCon2/qdnaseq/statistics.out", + "PosCon2/wisecondorx/PosCon2.wisecondorx_aberrations.bed", + "PosCon2/wisecondorx/PosCon2.wisecondorx_bins.bed", + "PosCon2/wisecondorx/PosCon2.wisecondorx_segments.bed", + "PosCon2/wisecondorx/PosCon2.wisecondorx_statistics.txt", + "PosCon2/wisecondorx/chr1.png", + "PosCon2/wisecondorx/chr22.png", + "PosCon2/wisecondorx/genome_wide.png", "PosCon3/PosCon3.cnv.vcf.gz", "PosCon3/PosCon3.cnv.vcf.gz.tbi", - "PosCon3/PosCon3.qdnaseq.qdnaseq.bed", - "PosCon3/PosCon3.qdnaseq.qdnaseq_segments.txt", - "PosCon3/PosCon3.qdnaseq.statistics.out", "PosCon3/PosCon3.repeats.vcf.gz", "PosCon3/PosCon3.repeats.vcf.gz.tbi", "PosCon3/PosCon3.sv.vcf.gz", "PosCon3/PosCon3.sv.vcf.gz.tbi", - "PosCon3/PosCon3.wisecondorx.chr1.png", - "PosCon3/PosCon3.wisecondorx.chr22.png", - "PosCon3/PosCon3.wisecondorx.genome_wide.png", - "PosCon3/PosCon3.wisecondorx.wisecondorx_aberrations.bed", - "PosCon3/PosCon3.wisecondorx.wisecondorx_bins.bed", - "PosCon3/PosCon3.wisecondorx.wisecondorx_segments.bed", - "PosCon3/PosCon3.wisecondorx.wisecondorx_statistics.txt", + "PosCon3/qdnaseq/PosCon3.qdnaseq.bed", + "PosCon3/qdnaseq/PosCon3.qdnaseq_segments.txt", + "PosCon3/qdnaseq/statistics.out", + "PosCon3/wisecondorx/PosCon3.wisecondorx_aberrations.bed", + "PosCon3/wisecondorx/PosCon3.wisecondorx_bins.bed", + "PosCon3/wisecondorx/PosCon3.wisecondorx_segments.bed", + "PosCon3/wisecondorx/PosCon3.wisecondorx_statistics.txt", + "PosCon3/wisecondorx/chr1.png", + "PosCon3/wisecondorx/chr22.png", + "PosCon3/wisecondorx/genome_wide.png", "multiqc/multiqc_report.html", "samplesheet.csv", "test_family/test_family.cnv.vcf.gz", @@ -188,10 +188,10 @@ ] ], "meta": { - "nf-test": "0.9.1", - "nextflow": "24.10.3" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2025-02-04T14:46:56.098262494" + "timestamp": "2025-07-10T16:26:32.438276554" }, "family with 3 samples - concat": { "content": [ @@ -199,42 +199,42 @@ ], [ - "PosCon1/PosCon1.qdnaseq.qdnaseq.bed", - "PosCon1/PosCon1.qdnaseq.qdnaseq_segments.txt", - "PosCon1/PosCon1.qdnaseq.statistics.out", "PosCon1/PosCon1.vcf.gz", "PosCon1/PosCon1.vcf.gz.tbi", - "PosCon1/PosCon1.wisecondorx.chr1.png", - "PosCon1/PosCon1.wisecondorx.chr22.png", - "PosCon1/PosCon1.wisecondorx.genome_wide.png", - "PosCon1/PosCon1.wisecondorx.wisecondorx_aberrations.bed", - "PosCon1/PosCon1.wisecondorx.wisecondorx_bins.bed", - "PosCon1/PosCon1.wisecondorx.wisecondorx_segments.bed", - "PosCon1/PosCon1.wisecondorx.wisecondorx_statistics.txt", - "PosCon2/PosCon2.qdnaseq.qdnaseq.bed", - "PosCon2/PosCon2.qdnaseq.qdnaseq_segments.txt", - "PosCon2/PosCon2.qdnaseq.statistics.out", + "PosCon1/qdnaseq/PosCon1.qdnaseq.bed", + "PosCon1/qdnaseq/PosCon1.qdnaseq_segments.txt", + "PosCon1/qdnaseq/statistics.out", + "PosCon1/wisecondorx/PosCon1.wisecondorx_aberrations.bed", + "PosCon1/wisecondorx/PosCon1.wisecondorx_bins.bed", + "PosCon1/wisecondorx/PosCon1.wisecondorx_segments.bed", + "PosCon1/wisecondorx/PosCon1.wisecondorx_statistics.txt", + "PosCon1/wisecondorx/chr1.png", + "PosCon1/wisecondorx/chr22.png", + "PosCon1/wisecondorx/genome_wide.png", "PosCon2/PosCon2.vcf.gz", "PosCon2/PosCon2.vcf.gz.tbi", - "PosCon2/PosCon2.wisecondorx.chr1.png", - "PosCon2/PosCon2.wisecondorx.chr22.png", - "PosCon2/PosCon2.wisecondorx.genome_wide.png", - "PosCon2/PosCon2.wisecondorx.wisecondorx_aberrations.bed", - "PosCon2/PosCon2.wisecondorx.wisecondorx_bins.bed", - "PosCon2/PosCon2.wisecondorx.wisecondorx_segments.bed", - "PosCon2/PosCon2.wisecondorx.wisecondorx_statistics.txt", - "PosCon3/PosCon3.qdnaseq.qdnaseq.bed", - "PosCon3/PosCon3.qdnaseq.qdnaseq_segments.txt", - "PosCon3/PosCon3.qdnaseq.statistics.out", + "PosCon2/qdnaseq/PosCon2.qdnaseq.bed", + "PosCon2/qdnaseq/PosCon2.qdnaseq_segments.txt", + "PosCon2/qdnaseq/statistics.out", + "PosCon2/wisecondorx/PosCon2.wisecondorx_aberrations.bed", + "PosCon2/wisecondorx/PosCon2.wisecondorx_bins.bed", + "PosCon2/wisecondorx/PosCon2.wisecondorx_segments.bed", + "PosCon2/wisecondorx/PosCon2.wisecondorx_statistics.txt", + "PosCon2/wisecondorx/chr1.png", + "PosCon2/wisecondorx/chr22.png", + "PosCon2/wisecondorx/genome_wide.png", "PosCon3/PosCon3.vcf.gz", "PosCon3/PosCon3.vcf.gz.tbi", - "PosCon3/PosCon3.wisecondorx.chr1.png", - "PosCon3/PosCon3.wisecondorx.chr22.png", - "PosCon3/PosCon3.wisecondorx.genome_wide.png", - "PosCon3/PosCon3.wisecondorx.wisecondorx_aberrations.bed", - "PosCon3/PosCon3.wisecondorx.wisecondorx_bins.bed", - "PosCon3/PosCon3.wisecondorx.wisecondorx_segments.bed", - "PosCon3/PosCon3.wisecondorx.wisecondorx_statistics.txt", + "PosCon3/qdnaseq/PosCon3.qdnaseq.bed", + "PosCon3/qdnaseq/PosCon3.qdnaseq_segments.txt", + "PosCon3/qdnaseq/statistics.out", + "PosCon3/wisecondorx/PosCon3.wisecondorx_aberrations.bed", + "PosCon3/wisecondorx/PosCon3.wisecondorx_bins.bed", + "PosCon3/wisecondorx/PosCon3.wisecondorx_segments.bed", + "PosCon3/wisecondorx/PosCon3.wisecondorx_statistics.txt", + "PosCon3/wisecondorx/chr1.png", + "PosCon3/wisecondorx/chr22.png", + "PosCon3/wisecondorx/genome_wide.png", "multiqc/multiqc_report.html", "samplesheet.csv", "test_family/test_family.vcf.gz", @@ -242,9 +242,9 @@ ] ], "meta": { - "nf-test": "0.9.1", - "nextflow": "24.10.3" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2025-02-04T14:48:12.591568647" + "timestamp": "2025-07-10T16:27:38.837477412" } } \ No newline at end of file From 724f5a8849b12e5215160bc180badb5a0bc88b62 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 10 Jul 2025 16:35:10 +0200 Subject: [PATCH 3/3] update changelog --- CHANGELOG.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 29543936..34faf3bc 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -19,10 +19,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 4. Updated to nf-core template v3.2.0 5. Fixed language server errors 6. Removed the old output publishing code and used the new workflow output definitions instead -7. Bumped the minimal nextflow version to 24.10.0 +7. Bumped the minimal nextflow version to 25.04.0 8. VCFanno will now run when `--vcfanno_toml` has been given and `--annotate` has not been given. You still need to supply `--annotate` to get the full annotation, but this can be used check for common variants without having to perform full annotation. 9. Changed the `--annotations_filter` parameter to a `--filter` parameter. This parameter takes an argument of `bcftools filter` to filter the resulting VCFs. 10. Removed the `--delly_sv_types` parameter. +11. Moved all `wisecondorx` and `qdnaseq` outputs to a separate directory in each sample output. ### `Fixed`