\n\n[](https://github.com/nf-core/raredisease/actions/workflows/ci.yml)\n\n[](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[](https://nf-co.re/raredisease/results)[](https://doi.org/10.5281/zenodo.7995798)\n[](https://www.nf-test.com)\n[](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[](https://nf-co.re/raredisease/results)[](https://doi.org/10.5281/zenodo.7995798)\n\n[](https://www.nextflow.io/)\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/raredisease)\n\n[](https://nfcore.slack.com/channels/raredisease)[](https://twitter.com/nf_core)[](https://mstdn.science/@nf_core)[](https://www.youtube.com/c/nf-core)\n\n#### TOC\n\n- [Introduction](#introduction)\n- [Pipeline summary](#pipeline-summary)\n- [Usage](#usage)\n- [Pipeline output](#pipeline-output)\n- [Credits](#credits)\n- [Contributions and Support](#contributions-and-support)\n- [Citations](#citations)\n\n## Introduction\n\n**nf-core/raredisease** is a best-practice bioinformatic pipeline for calling and scoring variants from WGS/WES data from rare disease patients. This pipeline is heavily inspired by [MIP](https://github.com/Clinical-Genomics/MIP).\n\nThe pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted 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\nOn release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/raredisease/results).\n\n## Pipeline summary\n\n \n \n \n \n\n**1. Metrics:**\n\n- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)\n- [Mosdepth](https://github.com/brentp/mosdepth)\n- [MultiQC](http://multiqc.info/)\n- [Picard's CollectMutipleMetrics, CollectHsMetrics, and CollectWgsMetrics](https://broadinstitute.github.io/picard/)\n- [Qualimap](http://qualimap.conesalab.org/)\n- [Sentieon's WgsMetricsAlgo](https://support.sentieon.com/manual/usages/general/)\n- [TIDDIT's cov](https://github.com/J35P312/)\n\n**2. Alignment:**\n\n- [Bwa-mem2](https://github.com/bwa-mem2/bwa-mem2)\n- [BWA-MEME](https://github.com/kaist-ina/BWA-MEME)\n- [BWA](https://github.com/lh3/bwa)\n- [Sentieon DNAseq](https://support.sentieon.com/manual/DNAseq_usage/dnaseq/)\n\n**3. Variant calling - SNV:**\n\n- [DeepVariant](https://github.com/google/deepvariant)\n- [Sentieon DNAscope](https://support.sentieon.com/manual/DNAscope_usage/dnascope/)\n\n**4. Variant calling - SV:**\n\n- [Manta](https://github.com/Illumina/manta)\n- [TIDDIT's sv](https://github.com/SciLifeLab/TIDDIT)\n- Copy number variant calling:\n - [CNVnator](https://github.com/abyzovlab/CNVnator)\n - [GATK GermlineCNVCaller](https://github.com/broadinstitute/gatk)\n\n**5. Annotation - SNV:**\n\n- [bcftools roh](https://samtools.github.io/bcftools/bcftools.html#roh)\n- [vcfanno](https://github.com/brentp/vcfanno)\n- [CADD](https://cadd.gs.washington.edu/)\n- [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n- [UPD](https://github.com/bjhall/upd)\n- [Chromograph](https://github.com/Clinical-Genomics/chromograph)\n\n**6. Annotation - SV:**\n\n- [SVDB query](https://github.com/J35P312/SVDB#Query)\n- [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n\n**7. Mitochondrial analysis:**\n\n- [Alignment and variant calling - GATK Mitochondrial short variant discovery pipeline ](https://gatk.broadinstitute.org/hc/en-us/articles/4403870837275-Mitochondrial-short-variant-discovery-SNVs-Indels-)\n- [eKLIPse](https://github.com/dooguypapua/eKLIPse/tree/master)\n- Annotation:\n - [HaploGrep2](https://github.com/seppinho/haplogrep-cmd)\n - [Hmtnote](https://github.com/robertopreste/HmtNote)\n - [vcfanno](https://github.com/brentp/vcfanno)\n - [CADD](https://cadd.gs.washington.edu/)\n - [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n\n**8. Variant calling - repeat expansions:**\n\n- [Expansion Hunter](https://github.com/Illumina/ExpansionHunter)\n- [Stranger](https://github.com/Clinical-Genomics/stranger)\n\n**9. Variant calling - mobile elements:**\n\n- [RetroSeq](https://github.com/tk2/RetroSeq)\n\n**10. Rank variants - SV and SNV:**\n\n- [GENMOD](https://github.com/Clinical-Genomics/genmod)\n\n**11. Variant evaluation:**\n\n- [RTG Tools](https://github.com/RealTimeGenomics/rtg-tools)\n\nNote that it is possible to include/exclude certain tools or steps.\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,lane,fastq_1,fastq_2,sex,phenotype,paternal_id,maternal_id,case_id\nhugelymodelbat,1,reads_1.fastq.gz,reads_2.fastq.gz,1,2,,,justhusky\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\nSecond, ensure that you have defined the path to reference files and parameters required for the type of analysis that you want to perform. More information about this can be found [here](https://github.com/nf-core/raredisease/blob/dev/docs/usage.md).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/raredisease \\\n -profile \\\n --input samplesheet.csv \\\n --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\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/raredisease/usage) and the [parameter documentation](https://nf-co.re/raredisease/parameters).\n\n## Pipeline output\n\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/raredisease/output).\n\n## Credits\n\nnf-core/raredisease was written in a collaboration between the Clinical Genomics nodes in Sweden, with major contributions from [Ramprasad Neethiraj](https://github.com/ramprasadn), [Anders Jemt](https://github.com/jemten), [Lucia Pena Perez](https://github.com/Lucpen), and [Mei Wu](https://github.com/projectoriented) at Clinical Genomics Stockholm.\n\nAdditional contributors were [Sima Rahimi](https://github.com/sima-r), [Gwenna Breton](https://github.com/Gwennid) and [Emma V\u00e4sterviga](https://github.com/EmmaCAndersson) (Clinical Genomics Gothenburg); [Halfdan Rydbeck](https://github.com/hrydbeck) and [Lauri Mesilaakso](https://github.com/ljmesi) (Clinical Genomics Link\u00f6ping); [Subazini Thankaswamy Kosalai](https://github.com/sysbiocoder) (Clinical Genomics \u00d6rebro); [Annick Renevey](https://github.com/rannick), [Peter Pruisscher](https://github.com/peterpru) and [Eva Caceres](https://github.com/fevac) (Clinical Genomics Stockholm); [Ryan Kennedy](https://github.com/ryanjameskennedy) (Clinical Genomics Lund); [Anders Sune Pedersen](https://github.com/asp8200) (Danish National Genome Center) and [Lucas Taniguti](https://github.com/lmtani).\n\nWe thank the nf-core community 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\nFor further information or help, don't hesitate to get in touch on the [Slack `#raredisease` channel](https://nfcore.slack.com/channels/raredisease) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/raredisease for your analysis, please cite it using the following doi: [10.5281/zenodo.7995798](https://doi.org/10.5281/zenodo.7995798)\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\nYou can read more about MIP's use in healthcare in,\n\n> Stranneheim H, Lagerstedt-Robinson K, Magnusson M, et al. Integration of whole genome sequencing into a healthcare setting: high diagnostic rates across multiple clinical entities in 3219 rare disease patients. Genome Med. 2021;13(1):40. doi:10.1186/s13073-021-00855-5\n",
+ "datePublished": "2025-05-23T07:59:34+00:00",
+ "description": "
\n \n \n \n \n
\n\n[](https://github.com/nf-core/raredisease/actions/workflows/ci.yml)\n\n[](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[](https://nf-co.re/raredisease/results)[](https://doi.org/10.5281/zenodo.7995798)\n[](https://www.nf-test.com)\n[](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[](https://nf-co.re/raredisease/results)[](https://doi.org/10.5281/zenodo.7995798)\n\n[](https://www.nextflow.io/)\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/raredisease)\n\n[](https://nfcore.slack.com/channels/raredisease)[](https://twitter.com/nf_core)[](https://mstdn.science/@nf_core)[](https://www.youtube.com/c/nf-core)\n\n#### TOC\n\n- [Introduction](#introduction)\n- [Pipeline summary](#pipeline-summary)\n- [Usage](#usage)\n- [Pipeline output](#pipeline-output)\n- [Credits](#credits)\n- [Contributions and Support](#contributions-and-support)\n- [Citations](#citations)\n\n## Introduction\n\n**nf-core/raredisease** is a best-practice bioinformatic pipeline for calling and scoring variants from WGS/WES data from rare disease patients. This pipeline is heavily inspired by [MIP](https://github.com/Clinical-Genomics/MIP).\n\n> [!NOTE]\n> We do not support single-end data from Illumina, as some tools in the pipeline are not compatible with this type of data.\n\nThe pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted 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\nOn release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/raredisease/results).\n\n## Pipeline summary\n\n \n \n \n \n\n**1. Metrics:**\n\n- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)\n- [Mosdepth](https://github.com/brentp/mosdepth)\n- [MultiQC](http://multiqc.info/)\n- [Picard's CollectMutipleMetrics, CollectHsMetrics, and CollectWgsMetrics](https://broadinstitute.github.io/picard/)\n- [Qualimap](http://qualimap.conesalab.org/)\n- [Sentieon's WgsMetricsAlgo](https://support.sentieon.com/manual/usages/general/)\n- [TIDDIT's cov](https://github.com/J35P312/)\n- [VerifyBamID2](https://github.com/Griffan/VerifyBamID)\n\n**2. Alignment:**\n\n- [Bwa-mem2](https://github.com/bwa-mem2/bwa-mem2)\n- [BWA-MEME](https://github.com/kaist-ina/BWA-MEME)\n- [BWA](https://github.com/lh3/bwa)\n- [Sentieon DNAseq](https://support.sentieon.com/manual/DNAseq_usage/dnaseq/)\n\n**3. Variant calling - SNV:**\n\n- [DeepVariant](https://github.com/google/deepvariant)\n- [Sentieon DNAscope](https://support.sentieon.com/manual/DNAscope_usage/dnascope/)\n\n**4. Variant calling - SV:**\n\n- [Manta](https://github.com/Illumina/manta)\n- [TIDDIT's sv](https://github.com/SciLifeLab/TIDDIT)\n- Copy number variant calling:\n - [CNVnator](https://github.com/abyzovlab/CNVnator)\n - [GATK GermlineCNVCaller](https://github.com/broadinstitute/gatk)\n\n**5. Annotation - SNV:**\n\n- [bcftools roh](https://samtools.github.io/bcftools/bcftools.html#roh)\n- [vcfanno](https://github.com/brentp/vcfanno)\n- [CADD](https://cadd.gs.washington.edu/)\n- [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n- [UPD](https://github.com/bjhall/upd)\n- [Chromograph](https://github.com/Clinical-Genomics/chromograph)\n\n**6. Annotation - SV:**\n\n- [SVDB query](https://github.com/J35P312/SVDB#Query)\n- [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n\n**7. Mitochondrial analysis:**\n\n- [Alignment and variant calling - GATK Mitochondrial short variant discovery pipeline ](https://gatk.broadinstitute.org/hc/en-us/articles/4403870837275-Mitochondrial-short-variant-discovery-SNVs-Indels-)\n- [eKLIPse](https://github.com/dooguypapua/eKLIPse/tree/master)\n- Annotation:\n - [HaploGrep2](https://github.com/seppinho/haplogrep-cmd)\n - [Hmtnote](https://github.com/robertopreste/HmtNote)\n - [vcfanno](https://github.com/brentp/vcfanno)\n - [CADD](https://cadd.gs.washington.edu/)\n - [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n\n**8. Variant calling - repeat expansions:**\n\n- [Expansion Hunter](https://github.com/Illumina/ExpansionHunter)\n- [Stranger](https://github.com/Clinical-Genomics/stranger)\n\n**9. Variant calling - mobile elements:**\n\n- [RetroSeq](https://github.com/tk2/RetroSeq)\n\n**10. Rank variants - SV and SNV:**\n\n- [GENMOD](https://github.com/Clinical-Genomics/genmod)\n\n**11. Variant evaluation:**\n\n- [RTG Tools](https://github.com/RealTimeGenomics/rtg-tools)\n\nNote that it is possible to include/exclude certain tools or steps.\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,lane,fastq_1,fastq_2,sex,phenotype,paternal_id,maternal_id,case_id\nhugelymodelbat,1,reads_1.fastq.gz,reads_2.fastq.gz,1,2,,,justhusky\n```\n\nEach row represents a pair of fastq files (paired end).\n\nSecond, ensure that you have defined the path to reference files and parameters required for the type of analysis that you want to perform. More information about this can be found [here](https://github.com/nf-core/raredisease/blob/dev/docs/usage.md).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/raredisease \\\n -profile \\\n --input samplesheet.csv \\\n --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\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/raredisease/usage) and the [parameter documentation](https://nf-co.re/raredisease/parameters).\n\n## Pipeline output\n\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/raredisease/output).\n\n## Credits\n\nnf-core/raredisease was written in a collaboration between the Clinical Genomics nodes in Sweden, with major contributions from [Ramprasad Neethiraj](https://github.com/ramprasadn), [Anders Jemt](https://github.com/jemten), [Lucia Pena Perez](https://github.com/Lucpen), and [Mei Wu](https://github.com/projectoriented) at Clinical Genomics Stockholm.\n\nAdditional contributors were [Sima Rahimi](https://github.com/sima-r), [Gwenna Breton](https://github.com/Gwennid) and [Emma V\u00e4sterviga](https://github.com/EmmaCAndersson) (Clinical Genomics Gothenburg); [Halfdan Rydbeck](https://github.com/hrydbeck) and [Lauri Mesilaakso](https://github.com/ljmesi) (Clinical Genomics Link\u00f6ping); [Subazini Thankaswamy Kosalai](https://github.com/sysbiocoder) (Clinical Genomics \u00d6rebro); [Annick Renevey](https://github.com/rannick), [Peter Pruisscher](https://github.com/peterpru) and [Eva Caceres](https://github.com/fevac) (Clinical Genomics Stockholm); [Ryan Kennedy](https://github.com/ryanjameskennedy) (Clinical Genomics Lund); [Anders Sune Pedersen](https://github.com/asp8200) (Danish National Genome Center) and [Lucas Taniguti](https://github.com/lmtani).\n\nWe thank the nf-core community 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\nFor further information or help, don't hesitate to get in touch on the [Slack `#raredisease` channel](https://nfcore.slack.com/channels/raredisease) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/raredisease for your analysis, please cite it using the following doi: [10.5281/zenodo.7995798](https://doi.org/10.5281/zenodo.7995798)\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\nYou can read more about MIP's use in healthcare in,\n\n> Stranneheim H, Lagerstedt-Robinson K, Magnusson M, et al. Integration of whole genome sequencing into a healthcare setting: high diagnostic rates across multiple clinical entities in 3219 rare disease patients. Genome Med. 2021;13(1):40. doi:10.1186/s13073-021-00855-5\n",
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- "dateModified": "2025-02-24T15:01:00Z",
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"@type": "TestSuite",
"instance": [
{
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"@type": "Person",
- "email": "Gwenna.breton@gu.se",
- "name": "Gwenna Breton"
+ "email": "lucia.pena.perez@scilifelab.se",
+ "name": "Luc\u00eda Pe\u00f1a-P\u00e9rez"
+ },
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+ "@id": "https://orcid.org/0000-0003-1316-2845",
+ "@type": "Person",
+ "email": "raysloks@gmail.com",
+ "name": "Emil Bertilsson"
},
{
"@id": "https://orcid.org/0000-0002-2219-0197",
@@ -399,10 +399,10 @@
"name": "Anders Jemt"
},
{
- "@id": "https://orcid.org/0000-0002-5044-7754",
+ "@id": "https://orcid.org/0000-0002-4100-9963",
"@type": "Person",
- "email": "lucia.pena.perez@scilifelab.se",
- "name": "Luc\u00eda Pe\u00f1a-P\u00e9rez"
+ "email": "Gwenna.breton@gu.se",
+ "name": "Gwenna Breton"
}
]
}
\ No newline at end of file
diff --git a/subworkflows/local/call_snv.nf b/subworkflows/local/call_snv.nf
index 33da6d418..eac3adfec 100644
--- a/subworkflows/local/call_snv.nf
+++ b/subworkflows/local/call_snv.nf
@@ -8,6 +8,7 @@ include { CALL_SNV_MT } from './call_snv_MT'
include { CALL_SNV_MT as CALL_SNV_MT_SHIFT } from './call_snv_MT'
include { POSTPROCESS_MT_CALLS } from './postprocess_MT_calls'
include { GATK4_SELECTVARIANTS } from '../../modules/nf-core/gatk4/selectvariants/main'
+include { BCFTOOLS_CONCAT } from '../../modules/nf-core/bcftools/concat'
workflow CALL_SNV {
take:
@@ -45,6 +46,7 @@ workflow CALL_SNV {
ch_deepvar_gtbi = Channel.empty()
ch_mt_vcf = Channel.empty()
ch_mt_tabix = Channel.empty()
+ ch_mt_vcf_tabix = Channel.empty()
ch_mt_txt = Channel.empty()
ch_sentieon_vcf = Channel.empty()
ch_sentieon_tbi = Channel.empty()
@@ -131,13 +133,22 @@ workflow CALL_SNV {
ch_foundin_header,
ch_genome_chrsizes
)
- ch_mt_vcf = POSTPROCESS_MT_CALLS.out.vcf
- ch_mt_tabix = POSTPROCESS_MT_CALLS.out.tbi
- ch_mt_txt = CALL_SNV_MT.out.txt
- ch_versions = ch_versions.mix(CALL_SNV_MT.out.versions)
- ch_versions = ch_versions.mix(CALL_SNV_MT_SHIFT.out.versions)
- ch_versions = ch_versions.mix(POSTPROCESS_MT_CALLS.out.versions)
- ch_versions = ch_versions.mix(GATK4_SELECTVARIANTS.out.versions)
+ ch_mt_vcf = POSTPROCESS_MT_CALLS.out.vcf
+ ch_mt_tabix = POSTPROCESS_MT_CALLS.out.tbi
+ ch_mt_vcf_tabix = ch_mt_vcf.join(ch_mt_tabix, failOnMismatch:true, failOnDuplicate:true)
+ ch_mt_txt = CALL_SNV_MT.out.txt
+ ch_versions = ch_versions.mix(CALL_SNV_MT.out.versions)
+ ch_versions = ch_versions.mix(CALL_SNV_MT_SHIFT.out.versions)
+ ch_versions = ch_versions.mix(POSTPROCESS_MT_CALLS.out.versions)
+ ch_versions = ch_versions.mix(GATK4_SELECTVARIANTS.out.versions)
+ }
+
+ if (params.concatenate_snv_calls) {
+ ch_concat_vcf_in = ch_genome_vcf_tabix.concat(ch_mt_vcf_tabix).groupTuple()
+ BCFTOOLS_CONCAT (
+ ch_concat_vcf_in
+ )
+ ch_versions = ch_versions.mix(BCFTOOLS_CONCAT.out.versions)
}
emit:
diff --git a/subworkflows/local/call_snv_deepvariant/main.nf b/subworkflows/local/call_snv_deepvariant/main.nf
index 9cfb63899..2623ab7b2 100644
--- a/subworkflows/local/call_snv_deepvariant/main.nf
+++ b/subworkflows/local/call_snv_deepvariant/main.nf
@@ -40,9 +40,9 @@ workflow CALL_SNV_DEEPVARIANT {
DEEPVARIANT ( ch_deepvar_in, ch_genome_fasta, ch_genome_fai, [[],[]], ch_par_bed )
DEEPVARIANT.out.gvcf
- .collect{it[1]}
+ .map{ it -> it[1]}
+ .toSortedList{a, b -> a.name <=> b.name}
.toList()
- .collect()
.set { ch_file_list }
ch_case_info
diff --git a/subworkflows/local/generate_cytosure_files.nf b/subworkflows/local/generate_cytosure_files.nf
index 14d74023a..569300db2 100644
--- a/subworkflows/local/generate_cytosure_files.nf
+++ b/subworkflows/local/generate_cytosure_files.nf
@@ -28,15 +28,16 @@ workflow GENERATE_CYTOSURE_FILES {
ch_bam.combine(ch_vcf_tbi)
.map {
meta_sample, bam, meta_case, vcf, tbi ->
- def new_meta = ['id':meta_sample.sample, 'sex':meta_sample.sex]
- return [ new_meta, vcf, tbi ]
+ id_meta = ['id':meta_sample.sample]
+ sex_meta = ['sex':meta_sample.sex]
+ return [ id_meta, sex_meta, vcf, tbi ]
}
.join(ch_sample_id_map, remainder: true)
.branch { it ->
- id: it[3].equals(null)
- return [it[0] + [custid:it[0].id], it[1], it[2]]
- custid: !(it[3].equals(null))
- return [it[0] + [custid:it[3]], it[1], it[2]]
+ id: it[4].equals(null)
+ return [it[0] + [custid:it[0].id] + it[1], it[2], it[3]]
+ custid: !(it[4].equals(null))
+ return [it[0] + [custid:it[4]] + it[1], it[2], it[3]]
}
.set { ch_for_mix }
@@ -71,11 +72,18 @@ workflow GENERATE_CYTOSURE_FILES {
Channel.empty()
.mix(ch_for_mix.split, ch_for_mix.reheader)
+ .toSortedList { a, b -> a[0].id <=> b[0].id }
+ .flatMap()
.set { ch_vcf2cytosure_in }
+ TIDDIT_COV_VCF2CYTOSURE.out.cov
+ .toSortedList { a, b -> a[0].id <=> b[0].id }
+ .flatMap()
+ .set { ch_cov2cytosure_in }
+
VCF2CYTOSURE (
ch_vcf2cytosure_in,
- TIDDIT_COV_VCF2CYTOSURE.out.cov,
+ ch_cov2cytosure_in,
[[:], []], [[:], []],
ch_blacklist
)
diff --git a/subworkflows/local/postprocess_MT_calls/main.nf b/subworkflows/local/postprocess_MT_calls/main.nf
index 9978ca292..6cd32fec6 100644
--- a/subworkflows/local/postprocess_MT_calls/main.nf
+++ b/subworkflows/local/postprocess_MT_calls/main.nf
@@ -41,8 +41,9 @@ workflow POSTPROCESS_MT_CALLS {
ch_vcfs = ch_mt_vcf
.join(PICARD_LIFTOVERVCF.out.vcf_lifted, remainder: true)
.map{ meta, vcf1, vcf2 ->
- [meta, [vcf1, vcf2]]
- }
+ [meta, [vcf1, vcf2]]
+ }
+
GATK4_MERGEVCFS_LIFT_UNLIFT_MT( ch_vcfs, ch_genome_dictionary)
// Filtering Variants
@@ -66,14 +67,14 @@ workflow POSTPROCESS_MT_CALLS {
TABIX_TABIX_MT2(REMOVE_DUPLICATES_MT.out.vcf)
REMOVE_DUPLICATES_MT.out.vcf
- .collect{it[1]}
- .ifEmpty([])
+ .map{ it -> it[1]}
+ .toSortedList{a, b -> a.name <=> b.name}
.toList()
.set { file_list_vcf }
TABIX_TABIX_MT2.out.tbi
- .collect{it[1]}
- .ifEmpty([])
+ .map{ it -> it[1]}
+ .toSortedList{a, b -> a.name <=> b.name}
.toList()
.set { file_list_tbi }
diff --git a/subworkflows/local/qc_bam.nf b/subworkflows/local/qc_bam.nf
index 2b08eebb0..f4bb6ff51 100644
--- a/subworkflows/local/qc_bam.nf
+++ b/subworkflows/local/qc_bam.nf
@@ -14,6 +14,7 @@ include { PICARD_COLLECTWGSMETRICS as PICARD_COLLECTWGSMETRICS_Y } from '../..
include { SENTIEON_WGSMETRICS as SENTIEON_WGSMETRICS_WG } from '../../modules/nf-core/sentieon/wgsmetrics/main'
include { SENTIEON_WGSMETRICS as SENTIEON_WGSMETRICS_Y } from '../../modules/nf-core/sentieon/wgsmetrics/main'
include { NGSBITS_SAMPLEGENDER } from '../../modules/nf-core/ngsbits/samplegender/main'
+include { VERIFYBAMID_VERIFYBAMID2 } from '../../modules/nf-core/verifybamid/verifybamid2/main'
workflow QC_BAM {
@@ -28,7 +29,10 @@ workflow QC_BAM {
ch_chrom_sizes // channel: [mandatory] [ path(sizes) ]
ch_intervals_wgs // channel: [mandatory] [ path(intervals) ]
ch_intervals_y // channel: [mandatory] [ path(intervals) ]
- ngsbits_samplegender_method // channel [val(method)]
+ ch_svd_bed // channel: [optional] [ path(bed) ]
+ ch_svd_mu // channel: [optional] [ path(meanpath) ]
+ ch_svd_ud // channel: [optional] [ path(ud) ]
+ ngsbits_samplegender_method // channel: [val(method)]
main:
ch_cov = Channel.empty()
@@ -71,6 +75,9 @@ workflow QC_BAM {
// Check sex
NGSBITS_SAMPLEGENDER(ch_bam_bai, ch_genome_fasta, ch_genome_fai, ngsbits_samplegender_method)
+ // Check contamination
+ ch_svd_in = ch_svd_ud.combine(ch_svd_mu).combine(ch_svd_bed).collect()
+ VERIFYBAMID_VERIFYBAMID2(ch_bam_bai, ch_svd_in, [], ch_genome_fasta.map {it-> it[1]})
ch_versions = ch_versions.mix(CHROMOGRAPH_COV.out.versions.first())
ch_versions = ch_versions.mix(PICARD_COLLECTMULTIPLEMETRICS.out.versions.first())
@@ -79,6 +86,7 @@ workflow QC_BAM {
ch_versions = ch_versions.mix(UCSC_WIGTOBIGWIG.out.versions.first())
ch_versions = ch_versions.mix(MOSDEPTH.out.versions.first())
ch_versions = ch_versions.mix(NGSBITS_SAMPLEGENDER.out.versions.first())
+ ch_versions = ch_versions.mix(VERIFYBAMID_VERIFYBAMID2.out.versions.first())
emit:
multiple_metrics = PICARD_COLLECTMULTIPLEMETRICS.out.metrics // channel: [ val(meta), path(metrics) ]
@@ -88,7 +96,8 @@ workflow QC_BAM {
bigwig = UCSC_WIGTOBIGWIG.out.bw // channel: [ val(meta), path(bw) ]
d4 = MOSDEPTH.out.per_base_d4 // channel: [ val(meta), path(d4) ]
global_dist = MOSDEPTH.out.global_txt // channel: [ val(meta), path(txt) ]
- sex_check = NGSBITS_SAMPLEGENDER.out.tsv // channel: [val(meta), path(tsv) ]
+ sex_check = NGSBITS_SAMPLEGENDER.out.tsv // channel: [ val(meta), path(tsv) ]
+ self_sm = VERIFYBAMID_VERIFYBAMID2.out.self_sm // channel: [ val(meta), path(selfSM) ]
cov = ch_cov // channel: [ val(meta), path(metrics) ]
cov_y = ch_cov_y // channel: [ val(meta), path(metrics) ]
versions = ch_versions // channel: [ path(versions.yml) ]
diff --git a/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf b/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf
index c089fe2a1..1fd4335d6 100644
--- a/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf
@@ -451,6 +451,7 @@ def toolCitationText() {
"Qualimap (Okonechnikov et al., 2016),",
"TIDDIT (Eisfeldt et al., 2017),",
"UCSC Bigwig and Bigbed (Kent et al., 2010),",
+ (params.verifybamid_svd_bed && params.verifybamid_svd_mu && params.verifybamid_svd_ud) ? "VerifyBamID2 (Zhang et al., 2020)," : "",
"Mosdepth (Pedersen & Quinlan, 2018),"
]
preprocessing_text = [
@@ -579,6 +580,7 @@ def toolBibliographyText() {
"
Okonechnikov, K., Conesa, A., & García-Alcalde, F. (2016). Qualimap 2: Advanced multi-sample quality control for high-throughput sequencing data. Bioinformatics, 32(2), 292–294. https://doi.org/10.1093/bioinformatics/btv566
",
"
Eisfeldt, J., Vezzi, F., Olason, P., Nilsson, D., & Lindstrand, A. (2017). TIDDIT, an efficient and comprehensive structural variant caller for massive parallel sequencing data. F1000Research, 6, 664. https://doi.org/10.12688/f1000research.11168.2
",
"
Kent, W. J., Zweig, A. S., Barber, G., Hinrichs, A. S., & Karolchik, D. (2010). BigWig and BigBed: Enabling browsing of large distributed datasets. Bioinformatics, 26(17), 2204–2207. https://doi.org/10.1093/bioinformatics/btq351
Zhang, F., Flickinger, M., Taliun, S. A. G., Consortium, I. P. G., Abecasis, G. R., Scott, L. J., McCaroll, S. A., Pato, C. N., Boehnke, M., & Kang, H. M. (2020). Ancestry-agnostic estimation of DNA sample contamination from sequence reads. Genome Research, 30(2), 185–194. https://doi.org/10.1101/gr.246934.118
" : "",
"
Pedersen, B. S., & Quinlan, A. R. (2018). Mosdepth: Quick coverage calculation for genomes and exomes. Bioinformatics, 34(5), 867–868. https://doi.org/10.1093/bioinformatics/btx699
![\"nf-core/raredisease\"](\"docs/images/nf-core-raredisease_logo_light.png\")
\n ![\"nf-core/raredisease\"](\"docs/images/nf-core-raredisease_logo_dark.png\"){kind=logo}
\n ![\"nf-core/raredisease](\"docs/images/raredisease_metromap_dark.png\")
\n