diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8c832c1..740b72b 100644
--- 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).
+## [dev]
+
+### `Added`
+
+- Added Zenodo DOI (10.5281/zenodo.21038367) for citation
+
## 1.0.0 - [2026-06-29]
Initial release of nf-core/rnadnavar.
diff --git a/README.md b/README.md
index d815c47..dfaa948 100644
--- a/README.md
+++ b/README.md
@@ -7,7 +7,7 @@
[](https://github.com/codespaces/new/nf-core/rnadnavar)
[](https://github.com/nf-core/rnadnavar/actions/workflows/nf-test.yml)
-[](https://github.com/nf-core/rnadnavar/actions/workflows/linting.yml)[](https://nf-co.re/rnadnavar/results)[](https://doi.org/10.5281/zenodo.XXXXXXX)
+[](https://github.com/nf-core/rnadnavar/actions/workflows/linting.yml)[](https://nf-co.re/rnadnavar/results)[](https://doi.org/10.5281/zenodo.21038367)
[](https://www.nf-test.com)
[](https://www.nextflow.io/)
@@ -185,7 +185,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
## Citations
-
+
An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
diff --git a/nextflow.config b/nextflow.config
index 10a76ab..b3879a6 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -391,7 +391,7 @@ manifest {
defaultBranch = 'master'
nextflowVersion = '!>=25.10.4'
version = '1.0.0'
- doi = ''
+ doi = '10.5281/zenodo.21038367'
}
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index 041a3df..decc526 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -23,7 +23,7 @@
"@type": "Dataset",
"creativeWorkStatus": "Stable",
"datePublished": "2026-06-23T13:10:48+00:00",
- "description": "
\n \n \n \n \n
\n\n[](https://github.com/codespaces/new/nf-core/rnadnavar)\n[](https://github.com/nf-core/rnadnavar/actions/workflows/nf-test.yml)\n[](https://github.com/nf-core/rnadnavar/actions/workflows/linting.yml)[](https://nf-co.re/rnadnavar/results)[](https://doi.org/10.5281/zenodo.XXXXXXX)\n[](https://www.nf-test.com)\n\n[](https://www.nextflow.io/)\n[](https://github.com/nf-core/tools/releases/tag/4.0.2)\n[](https://docs.conda.io/en/latest/)\n[](https://www.docker.com/)\n[](https://sylabs.io/docs/)\n[](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/rnadnavar)\n\n[](https://nfcore.slack.com/channels/rnadnavar)[](https://bsky.app/profile/nf-co.re)[](https://mstdn.science/@nf_core)[](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\nThe **nf-core/rnadnavar** is a bioinformatics best-practice\nanalysis pipeline for RNA somatic mutation detection\nable to perform in parallel.\n\nInitially designed for cancer research, the pipeline\nuses different variant calling algorithms and applies a\nconsensus approach. A final filtering stage, should\nprovide a set of annotated somatic variants.\n\nThe pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across\nmultiple compute infrastructures in a very portable\nmanner. It uses Docker/Singularity containers making\ninstallation trivial and results highly reproducible.\nThe [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this\npipeline uses one container per process which makes it\nmuch easier to maintain and update software\ndependencies. Where possible, these processes have been\nsubmitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!\n\n## Pipeline summary\n\nDepending on the options and samples provided, the\npipeline will run different tasks. This is controlled\nmainly through `--step` and `--tools` parameters. This\nis a summary of the possible tasks to run with the pipeline:\n\n- Quality control and trimming (enabled by\n `--trim_fastq` and runs [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and\n [`fastp`](https://github.com/OpenGene/fastp))\n- Map Reads to Reference (BWA-mem, BWA-mem2, dragmap\n and/or STAR)\n- GATK preprocessing for DNA and RNA bulk sequencing\n samples (`GATK MarkDuplicates`, `GATK SplitNCigarReads`,`GATK\nBaseRecalibrator` and `GATK ApplyBQSR`)\n- Summarise alignment statistics (`samtools stats`, `mosdepth`)\n- Variant calling (enabled with `--tools`)\n - `Mutect2`\n - `Strelka2`\n - `SAGE`\n- Annotation with `VEP` (enabled with `--tools` adding\n `vep`)\n- Normalisation of VCFs with VT (enabled with `--tools`\n adding `normalisation`)\n- Transformation of VCF to MAF and consensus of variant\n calling results (enabled with `--tools` adding\n `consensus`)\n- Filtering of MAF files applying optional gnomad,\n whitelisting and blacklisting (enabled with `--tools`\n adding `filtering`)\n- Realignment step where reads from regions where a variant\n was found will be extracted and re-processed, only for\n RNA due to higher levels of background noise (enabled\n with `--tools` adding `realignment`).\n- Filtering of MAF files specific for RNA (enabled with\n `--tools` adding `rna_filtering`)\n\n
\n \n
\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/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data.\n\n### Key requirements for the analysis\n\n- RNA tumor samples must be associated with a DNA normal sample using the same patient ID. DNA tumour sample is optional.\n- Sample types are specified with status: 0 (normal DNA), 1 (tumor DNA), 2 (tumor RNA)\n- Reference files are required for the analysis.\n\n### Quick Start\n\nThe typical command for running the pipeline is:\n\n```bash\nnextflow run nf-core/rnadnavar \\\n -r \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \\\n --genome \\\n --tools \n```\n\n### Pipeline Steps\n\nThe pipeline can start from different entry points but `tools` need to be specified to run. If you are planning to run the pipeline by stages please read [usage](docs/usage.md#starting-from-different-steps).\n\n### Input requirements\n\nYou will need to create a samplesheet with information about the samples you want to analyze. The samplesheet must be a comma-separated file with a header row.\n\nEssential columns are:\n\n- `patient` - Unique patient identifier\n- `status` - Sample type (0/1/2)\n- `sample` - Unique sample identifier\n- And one of these options:\n - if variant calling is going to be performed of these three options should be an input (_note that this is included in the `realignment` step by default_):\n - `fastq_1`, `fastq_2` - Paths to paired-end FASTQ files (for raw data) (this also needs `lane` column)\n - `bam`,`bai` - Paths to BAM files and indices (for pre-aligned data)\n - `cram`,`crai` - Paths to CRAM files and indices (for pre-aligned data)\n - if the starting step is from `consensus` and no `realignment` will be performed (add `--skip_tools 'realignment'` to your command or params file) then the input are VCF/MAF:\n - `caller` - Caller used to generate that MAF (to annotate it during the consensus approach)\n - `maf` - Paths to MAF file\n - if `realignment` is desired then please add `normal_id` and take a look to [usage](docs/usage.md#starting-from-different-steps).\n\nExamples CSVs:\n\nStarting from `mapping`:\n\n```csv\npatient,sample,status,lane,fastq_1,fastq_2\nPT1,DNA_NORMAL_SAMPLE,0,LX,DNA_NORMAL_SAMPLE_L002_R1_001.fastq.gz,DNA_NORMAL_SAMPLE1_L002_R2_001.fastq.gz\nPT1,DNA_TUMOUR_SAMPLE,1,LX,DNA_TUMOUR_SAMPLE_L002_R1_001.fastq.gz,DNA_TUMOUR_SAMPLE_L002_R2_001.fastq.gz\nPT1,RNA_TUMOUR_SAMPLE,2,LX,RNA_TUMOUR_SAMPLE_L002_R1_001.fastq.gz,RNA_TUMOUR_SAMPLE_L002_R2_001.fastq.gz\n```\n\nStarting from `consensus` no realignment:\n\n```csv\npatient,sample,status,caller,maf\nPT1,RNA_TUMOUR_SAMPLE_1,2,mutect,DNA_TUMOUR_SAMPLE_1.mutect.maf\nPT1,RNA_TUMOUR_SAMPLE_1,2,strelka,RNA_TUMOUR_SAMPLE_1.strelka.maf\nPT1,RNA_TUMOUR_SAMPLE_2,2,mutect,DNA_TUMOUR_SAMPLE_2.mutect.maf\nPT1,RNA_TUMOUR_SAMPLE_2,2,strelka,RNA_TUMOUR_SAMPLE_2.strelka.maf\n```\n\n### Parameters\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/running/run-pipelines#using-parameter-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/rnadnavar/usage) and the [parameter documentation](https://nf-co.re/rnadnavar/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/rnadnavar/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/rnadnavar/output).\n\n## Credits\n\nThe nf-core/rnadnavar was originally written by Raquel\nManzano Garcia at Cancer Research UK Cambridge Institute\nwith the continuous support of [Maxime U Garcia](https://github.com/maxulysse). The\nworkflow is based on\n[RNA-MuTect](https://github.com/broadinstitute/RNA_MUTECT_1.0-1) which was\noriginally published by [Yizhak, _et al_ 2019 (Science)](https://www.science.org/doi/10.1126/science.aaw0726)\n\nWe thank the following people for their assistance in the development of this pipeline:\nTBC\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#rnadnavar` channel](https://nfcore.slack.com/channels/rnadnavar) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\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",
+ "description": "
\n \n \n \n \n
\n\n[](https://github.com/codespaces/new/nf-core/rnadnavar)\n[](https://github.com/nf-core/rnadnavar/actions/workflows/nf-test.yml)\n[](https://github.com/nf-core/rnadnavar/actions/workflows/linting.yml)[](https://nf-co.re/rnadnavar/results)[](https://doi.org/10.5281/zenodo.21038367)\n[](https://www.nf-test.com)\n\n[](https://www.nextflow.io/)\n[](https://github.com/nf-core/tools/releases/tag/4.0.2)\n[](https://docs.conda.io/en/latest/)\n[](https://www.docker.com/)\n[](https://sylabs.io/docs/)\n[](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/rnadnavar)\n\n[](https://nfcore.slack.com/channels/rnadnavar)[](https://bsky.app/profile/nf-co.re)[](https://mstdn.science/@nf_core)[](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\nThe **nf-core/rnadnavar** is a bioinformatics best-practice\nanalysis pipeline for RNA somatic mutation detection\nable to perform in parallel.\n\nInitially designed for cancer research, the pipeline\nuses different variant calling algorithms and applies a\nconsensus approach. A final filtering stage, should\nprovide a set of annotated somatic variants.\n\nThe pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across\nmultiple compute infrastructures in a very portable\nmanner. It uses Docker/Singularity containers making\ninstallation trivial and results highly reproducible.\nThe [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this\npipeline uses one container per process which makes it\nmuch easier to maintain and update software\ndependencies. Where possible, these processes have been\nsubmitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!\n\n## Pipeline summary\n\nDepending on the options and samples provided, the\npipeline will run different tasks. This is controlled\nmainly through `--step` and `--tools` parameters. This\nis a summary of the possible tasks to run with the pipeline:\n\n- Quality control and trimming (enabled by\n `--trim_fastq` and runs [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and\n [`fastp`](https://github.com/OpenGene/fastp))\n- Map Reads to Reference (BWA-mem, BWA-mem2, dragmap\n and/or STAR)\n- GATK preprocessing for DNA and RNA bulk sequencing\n samples (`GATK MarkDuplicates`, `GATK SplitNCigarReads`,`GATK\nBaseRecalibrator` and `GATK ApplyBQSR`)\n- Summarise alignment statistics (`samtools stats`, `mosdepth`)\n- Variant calling (enabled with `--tools`)\n - `Mutect2`\n - `Strelka2`\n - `SAGE`\n- Annotation with `VEP` (enabled with `--tools` adding\n `vep`)\n- Normalisation of VCFs with VT (enabled with `--tools`\n adding `normalisation`)\n- Transformation of VCF to MAF and consensus of variant\n calling results (enabled with `--tools` adding\n `consensus`)\n- Filtering of MAF files applying optional gnomad,\n whitelisting and blacklisting (enabled with `--tools`\n adding `filtering`)\n- Realignment step where reads from regions where a variant\n was found will be extracted and re-processed, only for\n RNA due to higher levels of background noise (enabled\n with `--tools` adding `realignment`).\n- Filtering of MAF files specific for RNA (enabled with\n `--tools` adding `rna_filtering`)\n\n
\n \n
\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/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data.\n\n### Key requirements for the analysis\n\n- RNA tumor samples must be associated with a DNA normal sample using the same patient ID. DNA tumour sample is optional.\n- Sample types are specified with status: 0 (normal DNA), 1 (tumor DNA), 2 (tumor RNA)\n- Reference files are required for the analysis.\n\n### Quick Start\n\nThe typical command for running the pipeline is:\n\n```bash\nnextflow run nf-core/rnadnavar \\\n -r \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \\\n --genome \\\n --tools \n```\n\n### Pipeline Steps\n\nThe pipeline can start from different entry points but `tools` need to be specified to run. If you are planning to run the pipeline by stages please read [usage](docs/usage.md#starting-from-different-steps).\n\n### Input requirements\n\nYou will need to create a samplesheet with information about the samples you want to analyze. The samplesheet must be a comma-separated file with a header row.\n\nEssential columns are:\n\n- `patient` - Unique patient identifier\n- `status` - Sample type (0/1/2)\n- `sample` - Unique sample identifier\n- And one of these options:\n - if variant calling is going to be performed of these three options should be an input (_note that this is included in the `realignment` step by default_):\n - `fastq_1`, `fastq_2` - Paths to paired-end FASTQ files (for raw data) (this also needs `lane` column)\n - `bam`,`bai` - Paths to BAM files and indices (for pre-aligned data)\n - `cram`,`crai` - Paths to CRAM files and indices (for pre-aligned data)\n - if the starting step is from `consensus` and no `realignment` will be performed (add `--skip_tools 'realignment'` to your command or params file) then the input are VCF/MAF:\n - `caller` - Caller used to generate that MAF (to annotate it during the consensus approach)\n - `maf` - Paths to MAF file\n - if `realignment` is desired then please add `normal_id` and take a look to [usage](docs/usage.md#starting-from-different-steps).\n\nExamples CSVs:\n\nStarting from `mapping`:\n\n```csv\npatient,sample,status,lane,fastq_1,fastq_2\nPT1,DNA_NORMAL_SAMPLE,0,LX,DNA_NORMAL_SAMPLE_L002_R1_001.fastq.gz,DNA_NORMAL_SAMPLE1_L002_R2_001.fastq.gz\nPT1,DNA_TUMOUR_SAMPLE,1,LX,DNA_TUMOUR_SAMPLE_L002_R1_001.fastq.gz,DNA_TUMOUR_SAMPLE_L002_R2_001.fastq.gz\nPT1,RNA_TUMOUR_SAMPLE,2,LX,RNA_TUMOUR_SAMPLE_L002_R1_001.fastq.gz,RNA_TUMOUR_SAMPLE_L002_R2_001.fastq.gz\n```\n\nStarting from `consensus` no realignment:\n\n```csv\npatient,sample,status,caller,maf\nPT1,RNA_TUMOUR_SAMPLE_1,2,mutect,DNA_TUMOUR_SAMPLE_1.mutect.maf\nPT1,RNA_TUMOUR_SAMPLE_1,2,strelka,RNA_TUMOUR_SAMPLE_1.strelka.maf\nPT1,RNA_TUMOUR_SAMPLE_2,2,mutect,DNA_TUMOUR_SAMPLE_2.mutect.maf\nPT1,RNA_TUMOUR_SAMPLE_2,2,strelka,RNA_TUMOUR_SAMPLE_2.strelka.maf\n```\n\n### Parameters\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/running/run-pipelines#using-parameter-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/rnadnavar/usage) and the [parameter documentation](https://nf-co.re/rnadnavar/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/rnadnavar/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/rnadnavar/output).\n\n## Credits\n\nThe nf-core/rnadnavar was originally written by Raquel\nManzano Garcia at Cancer Research UK Cambridge Institute\nwith the continuous support of [Maxime U Garcia](https://github.com/maxulysse). The\nworkflow is based on\n[RNA-MuTect](https://github.com/broadinstitute/RNA_MUTECT_1.0-1) which was\noriginally published by [Yizhak, _et al_ 2019 (Science)](https://www.science.org/doi/10.1126/science.aaw0726)\n\nWe thank the following people for their assistance in the development of this pipeline:\nTBC\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#rnadnavar` channel](https://nfcore.slack.com/channels/rnadnavar) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\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": [
{
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![\"nf-core/rnadnavar\"](\"docs/images/nf-core-rnadnavar_logo_dark.png\"){kind=logo}
\n