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qbic-pipelines · Jan 8, 2025 · 297e6b4 · 297e6b4
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diff --git a/.nf-core.yml b/.nf-core.yml
@@ -1,33 +1,33 @@
 lint:
   files_exist:
-    - CODE_OF_CONDUCT.md
-    - assets/nf-core-vcftomat_logo_light.png
-    - docs/images/nf-core-vcftomat_logo_light.png
-    - docs/images/nf-core-vcftomat_logo_dark.png
-    - .github/ISSUE_TEMPLATE/config.yml
-    - .github/workflows/awstest.yml
-    - .github/workflows/awsfulltest.yml
+  - CODE_OF_CONDUCT.md
+  - assets/nf-core-vcftomat_logo_light.png
+  - docs/images/nf-core-vcftomat_logo_light.png
+  - docs/images/nf-core-vcftomat_logo_dark.png
+  - .github/ISSUE_TEMPLATE/config.yml
+  - .github/workflows/awstest.yml
+  - .github/workflows/awsfulltest.yml
   files_unchanged:
-    - .github/CONTRIBUTING.md
-    - .prettierignore
-    - .github/CONTRIBUTING.md
-    - .prettierignore
-    - CODE_OF_CONDUCT.md
-    - assets/nf-core-vcftomat_logo_light.png
-    - docs/images/nf-core-vcftomat_logo_light.png
-    - docs/images/nf-core-vcftomat_logo_dark.png
-    - .github/ISSUE_TEMPLATE/bug_report.yml
+  - .github/CONTRIBUTING.md
+  - .prettierignore
+  - .github/CONTRIBUTING.md
+  - .prettierignore
+  - CODE_OF_CONDUCT.md
+  - assets/nf-core-vcftomat_logo_light.png
+  - docs/images/nf-core-vcftomat_logo_light.png
+  - docs/images/nf-core-vcftomat_logo_dark.png
+  - .github/ISSUE_TEMPLATE/bug_report.yml
   included_configs: false
   actions_ci: false
   multiqc_config:
-    - report_comment
+  - report_comment
   nextflow_config:
-    - manifest.name
-    - manifest.homePage
-    - validation.help.beforeText
-    - validation.help.afterText
-    - validation.summary.beforeText
-    - validation.summary.afterText
+  - manifest.name
+  - manifest.homePage
+  - validation.help.beforeText
+  - validation.help.afterText
+  - validation.summary.beforeText
+  - validation.summary.afterText
 nf_core_version: 3.1.0
 repository_type: pipeline
 template:
@@ -40,8 +40,8 @@ template:
   org: qbic-pipelines
   outdir: .
   skip_features:
-    - gitpod
-    - codespaces
-    - fastqc
-    - adaptivecard
-  version: 1.1.0
+  - gitpod
+  - codespaces
+  - fastqc
+  - adaptivecard
+  version: 1.2.0dev
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,12 @@
 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).
 
+## v1.2.0dev
+
+### Added
+
+### Fixed
+
 ## v1.1.0 - Newton Puccoon - 08.01.2025
 
 ### Added

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -1,5 +1,5 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/qbic-pipelines/vcftomat/releases/tag/1.1.0"
+  This report has been generated by the <a href="https://github.com/qbic-pipelines/vcftomat/tree/dev"
   target="_blank">qbic-pipelines/vcftomat</a> analysis pipeline.
 report_section_order:
   "qbic-pipelines-vcftomat-methods-description":

diff --git a/nextflow.config b/nextflow.config
@@ -234,7 +234,7 @@ manifest {
     mainScript      = 'main.nf'
     defaultBranch   = 'master'
     nextflowVersion = '!>=24.04.2'
-    version         = '1.1.0'
+    version         = '1.2.0dev'
     doi             = ''
 }
 

diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
@@ -21,9 +21,9 @@
         {
             "@id": "./",
             "@type": "Dataset",
-            "creativeWorkStatus": "Stable",
-            "datePublished": "2025-01-08T12:21:55+00:00",
-            "description": "# qbic-pipelines/vcftomat\n\n[![GitHub Actions CI Status](https://github.com/qbic-pipelines/vcftomat/actions/workflows/ci.yml/badge.svg)](https://github.com/qbic-pipelines/vcftomat/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/qbic-pipelines/vcftomat/actions/workflows/linting.yml/badge.svg)](https://github.com/qbic-pipelines/vcftomat/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\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/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\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/vcftomat)\n\n## Introduction\n\n**qbic-pipelines/vcftomat** is a bioinformatics pipeline that processes g.vcf files to a matrix suitable for downstream analysis. The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps:\n\n1. Indexes (g.)vcf files ([`tabix`](http://www.htslib.org/doc/tabix.html))\n2. Converts g.vcf files to vcf with `genotypegvcf` ([`GATK`](https://gatk.broadinstitute.org/hc/en-us))\n3. Concatenates all vcfs that have the same id and the same label with `bcftools/concat` ([`bcftools`](https://samtools.github.io/bcftools/bcftools.html))\n4. Changes the sample name in the vcf file to the filename with `bcftools/reheader` ([`bcftools`](https://samtools.github.io/bcftools/bcftools.html)) - This can be turned off by adding `--rename false` to the `nextflow run` command.\n5. Merges all vcfs from the same sample with `bcftools/merge` ([`bcftools`](https://samtools.github.io/bcftools/bcftools.html))\n6. Converts the (merged) vcfs to a matrix using a custom R script written by @ellisdoro ([`R`](https://www.r-project.org/))\n7. Collects all reports into a MultiQC report ([`MultiQC`](http://multiqc.info/))\n\n![](./docs/images/vcftomat.excalidraw.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\nsample,label,gvcf,vcf_path,vcf_index_path\nSAMPLE-1,pipelineA-callerA,false,path/to/vcf.gz,path/to/.vcf.gz.tbi\nSAMPLE-1,pipelineB-callerA,false,path/to/vcf.gz,path/to/.vcf.gz.tbi\nSAMPLE-2,pipelineB-callerB,true,path/to/g.vcf.gz,path/to/g.vcf.gz.tbi\nSAMPLE-2,pipelineB-callerB,true,path/to/g.vcf.gz,path/to/g.vcf.gz.tbi\n```\n\nEach row represents a VCF file coming from a sample. The `label` column enables concatenation of vcfs (for example when the pipeline produces different vcfs for chrM and chrY). The `gvcf` column indicates whether the file is a g.vcf file or not. The `vcf_path` and `vcf_index_path` columns contain the path to the VCF file and its index, respectively.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run qbic-pipelines/vcftomat \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --genome GATK.GRCh38 \\\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/vcftomat was originally written by Famke B\u00e4uerle, Dorothy Ellis.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\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/vcftomat for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\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": "2025-01-08T14:48:05+00:00",
+            "description": "# qbic-pipelines/vcftomat\n\n[![GitHub Actions CI Status](https://github.com/qbic-pipelines/vcftomat/actions/workflows/ci.yml/badge.svg)](https://github.com/qbic-pipelines/vcftomat/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/qbic-pipelines/vcftomat/actions/workflows/linting.yml/badge.svg)](https://github.com/qbic-pipelines/vcftomat/actions/workflows/linting.yml)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.14616650-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.14616650)\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/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\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/vcftomat)\n\n## Introduction\n\n**qbic-pipelines/vcftomat** is a bioinformatics pipeline that processes g.vcf files to a matrix suitable for downstream analysis. The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps:\n\n1. Indexes (g.)vcf files ([`tabix`](http://www.htslib.org/doc/tabix.html))\n2. Converts g.vcf files to vcf with `genotypegvcf` ([`GATK`](https://gatk.broadinstitute.org/hc/en-us))\n3. Concatenates all vcfs that have the same id and the same label with `bcftools/concat` ([`bcftools`](https://samtools.github.io/bcftools/bcftools.html))\n4. Changes the sample name in the vcf file to the filename with `bcftools/reheader` ([`bcftools`](https://samtools.github.io/bcftools/bcftools.html)) - This can be turned off by adding `--rename false` to the `nextflow run` command.\n5. Merges all vcfs from the same sample with `bcftools/merge` ([`bcftools`](https://samtools.github.io/bcftools/bcftools.html))\n6. Converts the (merged) vcfs to a matrix using a custom R script written by @ellisdoro ([`R`](https://www.r-project.org/))\n7. Collects all reports into a MultiQC report ([`MultiQC`](http://multiqc.info/))\n\n![](./docs/images/vcftomat.excalidraw.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\nsample,label,gvcf,vcf_path,vcf_index_path\nSAMPLE-1,pipelineA-callerA,false,path/to/vcf.gz,path/to/.vcf.gz.tbi\nSAMPLE-1,pipelineB-callerA,false,path/to/vcf.gz,path/to/.vcf.gz.tbi\nSAMPLE-2,pipelineB-callerB,true,path/to/g.vcf.gz,path/to/g.vcf.gz.tbi\nSAMPLE-2,pipelineB-callerB,true,path/to/g.vcf.gz,path/to/g.vcf.gz.tbi\n```\n\nEach row represents a VCF file coming from a sample. The `label` column enables concatenation of vcfs (for example when the pipeline produces different vcfs for chrM and chrY). The `gvcf` column indicates whether the file is a g.vcf file or not. The `vcf_path` and `vcf_index_path` columns contain the path to the VCF file and its index, respectively.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run qbic-pipelines/vcftomat \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --genome GATK.GRCh38 \\\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/vcftomat was originally written by Famke B\u00e4uerle, Dorothy Ellis.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\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/vcftomat for your analysis, please cite it using the following doi: [10.5281/zenodo.14616650](https://doi.org/10.5281/zenodo.14616650)\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\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"
@@ -102,7 +102,7 @@
             },
             "mentions": [
                 {
-                    "@id": "#52a401c6-dec9-4dfe-92eb-d33149004223"
+                    "@id": "#a331573e-ab8a-4ef8-b58b-fce079a0219d"
                 }
             ],
             "name": "qbic-pipelines/vcftomat"
@@ -124,7 +124,11 @@
         },
         {
             "@id": "main.nf",
-            "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"],
+            "@type": [
+                "File",
+                "SoftwareSourceCode",
+                "ComputationalWorkflow"
+            ],
             "creator": [
                 {
                     "@id": "https://orcid.org/0000-0003-1387-0251"
@@ -134,24 +138,36 @@
                 }
             ],
             "dateCreated": "",
-            "dateModified": "2025-01-08T13:21:55Z",
+            "dateModified": "2025-01-08T15:48:05Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
-            "keywords": ["nf-core", "nextflow"],
-            "license": ["MIT"],
+            "keywords": [
+                "nf-core",
+                "nextflow"
+            ],
+            "license": [
+                "MIT"
+            ],
             "maintainer": [
                 {
                     "@id": "https://orcid.org/0000-0003-1387-0251"
                 }
             ],
-            "name": ["qbic-pipelines/vcftomat"],
+            "name": [
+                "qbic-pipelines/vcftomat"
+            ],
             "programmingLanguage": {
                 "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow"
             },
             "sdPublisher": {
                 "@id": "https://nf-co.re/"
             },
-            "url": ["https://github.com/qbic-pipelines/vcftomat", "https://nf-co.re/qbic-pipelines/vcftomat/1.1.0/"],
-            "version": ["1.1.0"]
+            "url": [
+                "https://github.com/qbic-pipelines/vcftomat",
+                "https://nf-co.re/qbic-pipelines/vcftomat/dev/"
+            ],
+            "version": [
+                "1.2.0dev"
+            ]
         },
         {
             "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow",
@@ -166,11 +182,11 @@
             "version": "!>=24.04.2"
         },
         {
-            "@id": "#52a401c6-dec9-4dfe-92eb-d33149004223",
+            "@id": "#a331573e-ab8a-4ef8-b58b-fce079a0219d",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#2a6b4982-255a-44b9-9ff1-e0690f6c6e9d"
+                    "@id": "#f9045bea-c5d1-4ad4-9246-ae0340086aaa"
                 }
             ],
             "mainEntity": {
@@ -179,7 +195,7 @@
             "name": "Test suite for qbic-pipelines/vcftomat"
         },
         {
-            "@id": "#2a6b4982-255a-44b9-9ff1-e0690f6c6e9d",
+            "@id": "#f9045bea-c5d1-4ad4-9246-ae0340086aaa",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing qbic-pipelines/vcftomat",
             "resource": "repos/qbic-pipelines/vcftomat/actions/workflows/ci.yml",
@@ -325,4 +341,4 @@
             "name": "Famke Ba\u0308uerle"
         }
     ]
-}
+}