Bump back to dev

.nf-core.yml

@@ -30,13 +30,13 @@ nf_core_version: 3.3.2
 repository_type: pipeline
 template:
   author: "Famke Baeuerle"
-  description: This pipeline takes multiple VCFs from different callers and
-    creates a consensus-based VCF.
+  description: This pipeline takes multiple VCFs from different callers and creates
+    a consensus-based VCF.
   force: false
   is_nfcore: false
   name: variantconsensus
   org: qbic-pipelines
   outdir: .
   skip_features:
     - fastqc
-  version: 1.0.0
+  version: 1.1.0dev

CHANGELOG.md

@@ -3,6 +3,16 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## v1.1.0dev
+
+### `Added`
+
+### `Fixed`
+
+### `Dependencies`
+
+### `Deprecated`
+
 ## v1.0.0 - 11.09.2025 - Alice Ball
 
 Initial release of qbic-pipelines/variantconsensus, created with the [nf-core](https://nf-co.re/) template.

assets/multiqc_config.yml

@@ -1,5 +1,5 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/qbic-pipelines/variantconsensus/releases/tag/1.0.0"
+  This report has been generated by the <a href="https://github.com/qbic-pipelines/variantconsensus/tree/dev"
   target="_blank">qbic-pipelines/variantconsensus</a> analysis pipeline.
 report_section_order:
   "qbic-pipelines-variantconsensus-methods-description":

nextflow.config

@@ -247,7 +247,7 @@ manifest {
     mainScript      = 'main.nf'
     defaultBranch   = 'master'
     nextflowVersion = '!>=24.10.5'
-    version         = '1.0.0'
+    version         = '1.1.0dev'
     doi             = ''
 }
 

ro-crate-metadata.json

@@ -21,9 +21,9 @@
         {
             "@id": "./",
             "@type": "Dataset",
-            "creativeWorkStatus": "Stable",
-            "datePublished": "2025-08-26T13:17:50+00:00",
-            "description": "# qbic-pipelines/variantconsensus\n\n[![GitHub Actions CI Status](https://github.com/qbic-pipelines/variantconsensus/actions/workflows/nf-test.yml/badge.svg)](https://github.com/qbic-pipelines/variantconsensus/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/qbic-pipelines/variantconsensus/actions/workflows/linting.yml/badge.svg)](https://github.com/qbic-pipelines/variantconsensus/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)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.10.5-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/qbic-pipelines/variantconsensus)\n\n## Introduction\n\n**qbic-pipelines/variantconsensus** is a bioinformatics pipeline that combines results from multiple variant callers to find a consensus VCF.\n\nInspired by\n\n> Trevarton, A. J., Chang, J. T., & Symmans, W. F. (2023). Simple combination of multiple somatic variant callers to increase accuracy. Scientific reports, 13(1), 8463.\n\n1. Split provided VCFs into SNPs and INDELS ([bcftools/view](https://samtools.github.io/bcftools/bcftools.html))\n2. Intersect SNPs / INDELs keeping only variants found in at least (N-1) / 2 of the provided VCFs ([bcftools/isec](https://samtools.github.io/bcftools/bcftools.html))\n3. Filter the consensus VCF for variants marked as 'PASS,.' ([bcftools/view](https://samtools.github.io/bcftools/bcftools.html))\n4. Report statistics for the filtered consensus VCFs ([bcftools/stats](https://samtools.github.io/bcftools/bcftools.html))\n5. Present statistics for variants ([`MultiQC`](http://multiqc.info/))\n\n![Subway Map](docs/subway.png)\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\npatient,sample,variantcaller,vcf,vcf_tbi,varianttype\nA,t5,strelka,https://github.com/qbic-pipelines/test-datasets/raw/refs/heads/main/variantconsensus/tumor_5_vs_normal_5.strelka.somatic_indels_VEP.ann.vcf.gz,https://github.com/qbic-pipelines/test-datasets/raw/refs/heads/main/variantconsensus/tumor_5_vs_normal_5.strelka.somatic_indels_VEP.ann.vcf.gz.tbi,indels\n```\n\nEach row represents a VCF file and its index. The varianttype can be either snps, indels or both.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run qbic-pipelines/variantconsensus \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\n## Credits\n\nqbic-pipelines/variantconsensus was originally written by Famke B\u00e4uerle.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use qbic-pipelines/variantconsensus for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nThis pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/main/LICENSE).\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
+            "creativeWorkStatus": "InProgress",
+            "datePublished": "2025-09-11T13:06:18+00:00",
+            "description": "# qbic-pipelines/variantconsensus\n\n[![GitHub Actions CI Status](https://github.com/qbic-pipelines/variantconsensus/actions/workflows/nf-test.yml/badge.svg)](https://github.com/qbic-pipelines/variantconsensus/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/qbic-pipelines/variantconsensus/actions/workflows/linting.yml/badge.svg)](https://github.com/qbic-pipelines/variantconsensus/actions/workflows/linting.yml)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.17100035-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.17100035)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.10.5-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/qbic-pipelines/variantconsensus)\n\n## Introduction\n\n**qbic-pipelines/variantconsensus** is a bioinformatics pipeline that combines results from multiple variant callers to find a consensus VCF.\n\nInspired by\n\n> Trevarton, A. J., Chang, J. T., & Symmans, W. F. (2023). Simple combination of multiple somatic variant callers to increase accuracy. Scientific reports, 13(1), 8463.\n\n1. Split provided VCFs into SNPs and INDELS ([bcftools/view](https://samtools.github.io/bcftools/bcftools.html))\n2. Intersect SNPs / INDELs keeping only variants found in at least (N-1) / 2 of the provided VCFs ([bcftools/isec](https://samtools.github.io/bcftools/bcftools.html))\n3. Filter the consensus VCF for variants marked as 'PASS,.' ([bcftools/view](https://samtools.github.io/bcftools/bcftools.html))\n4. Report statistics for the filtered consensus VCFs ([bcftools/stats](https://samtools.github.io/bcftools/bcftools.html))\n5. Present statistics for variants ([`MultiQC`](http://multiqc.info/))\n\n![Subway Map](docs/subway.png)\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\npatient,sample,variantcaller,vcf,vcf_tbi,varianttype\nA,t5,strelka,https://github.com/qbic-pipelines/test-datasets/raw/refs/heads/main/variantconsensus/tumor_5_vs_normal_5.strelka.somatic_indels_VEP.ann.vcf.gz,https://github.com/qbic-pipelines/test-datasets/raw/refs/heads/main/variantconsensus/tumor_5_vs_normal_5.strelka.somatic_indels_VEP.ann.vcf.gz.tbi,indels\n```\n\nEach row represents a VCF file and its index. The varianttype can be either snps, indels or both.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run qbic-pipelines/variantconsensus \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\n## Credits\n\nqbic-pipelines/variantconsensus was originally written by Famke B\u00e4uerle.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\n## Citations\n\nIf you use qbic-pipelines/variantconsensus for your analysis, please cite it using the following doi: [10.5281/zenodo.17100035](https://doi.org/10.5281/zenodo.17100035)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nThis pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/main/LICENSE).\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
             "hasPart": [
                 {
                     "@id": "main.nf"
@@ -93,7 +93,7 @@
             },
             "mentions": [
                 {
-                    "@id": "#2ff63cae-7a80-4823-a701-dfd66af9f307"
+                    "@id": "#b4dbe556-1080-48ff-8f78-804e5c481ee9"
                 }
             ],
             "name": "qbic-pipelines/variantconsensus"
@@ -122,11 +122,11 @@
             ],
             "creator": [
                 {
-                    "@id": "#famke.baeuerle@gmail.com"
+                    "@id": "#[email protected].com"
                 }
             ],
             "dateCreated": "",
-            "dateModified": "2025-08-26T15:17:50Z",
+            "dateModified": "2025-09-11T15:06:18Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
             "keywords": [
                 "nf-core",
@@ -146,10 +146,10 @@
             },
             "url": [
                 "https://github.com/qbic-pipelines/variantconsensus",
-                "https://nf-co.re/qbic-pipelines/variantconsensus/1.0.0/"
+                "https://nf-co.re/qbic-pipelines/variantconsensus/dev/"
             ],
             "version": [
-                "1.0.0"
+                "1.1.0dev"
             ]
         },
         {
@@ -165,11 +165,11 @@
             "version": "!>=24.10.5"
         },
         {
-            "@id": "#2ff63cae-7a80-4823-a701-dfd66af9f307",
+            "@id": "#b4dbe556-1080-48ff-8f78-804e5c481ee9",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#bc534a24-c9df-496b-8539-26a89eceeae4"
+                    "@id": "#b71bd365-2ef1-40e9-91af-9f7100810562"
                 }
             ],
             "mainEntity": {
@@ -178,7 +178,7 @@
             "name": "Test suite for qbic-pipelines/variantconsensus"
         },
         {
-            "@id": "#bc534a24-c9df-496b-8539-26a89eceeae4",
+            "@id": "#b71bd365-2ef1-40e9-91af-9f7100810562",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing qbic-pipelines/variantconsensus",
             "resource": "repos/qbic-pipelines/variantconsensus/actions/workflows/nf-test.yml",
@@ -297,9 +297,9 @@
             "url": "https://nf-co.re/"
         },
         {
-            "@id": "#famke.baeuerle@gmail.com",
+            "@id": "#[email protected].com",
             "@type": "Person",
-            "email": "famke.baeuerle@gmail.com",
+            "email": "[email protected].com",
             "name": "Famke Ba\u0308uerle"
         }
     ]

tests/default.nf.test.snap

@@ -28,7 +28,7 @@
                     "bcftools": 1.21
                 },
                 "Workflow": {
-                    "qbic-pipelines/variantconsensus": "v1.0.0"
+                    "qbic-pipelines/variantconsensus": "v1.1.0dev"
                 }
             },
             [
@@ -105,7 +105,7 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-08-26T15:25:14.327306493"
+        "timestamp": "2025-09-11T15:12:37.95489129"
     },
     "Params: default": {
         "content": [
@@ -136,7 +136,7 @@
                     "bcftools": 1.21
                 },
                 "Workflow": {
-                    "qbic-pipelines/variantconsensus": "v1.0.0"
+                    "qbic-pipelines/variantconsensus": "v1.1.0dev"
                 }
             },
             [
@@ -277,6 +277,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-08-26T15:24:59.968821797"
+        "timestamp": "2025-09-11T15:12:17.890992794"
     }
 }