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.nf-core.yml

@@ -39,4 +39,4 @@ template:
   org: genomic-medicine-sweden
   outdir: .
   skip_features: []
-  version: 0.5.0
+  version: 0.6.0dev

CHANGELOG.md

@@ -3,6 +3,38 @@
 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).
 
+## 0.6.0 - [XXXX-XX-XX]
+
+### `Added`
+
+### `Changed`
+
+- [#](https://github.com/genomic-medicine-sweden/nallo/pull/) - Updated version to 0.6.0dev
+
+### `Removed`
+
+### `Fixed`
+
+### Parameters
+
+| Old parameter | New parameter |
+| ------------- | ------------- |
+
+> [!NOTE]
+> Parameter has been updated if both old and new parameter information is present.
+> Parameter has been added if just the new parameter information is present.
+> Parameter has been removed if new parameter information isn't present.
+
+### Module updates
+
+| Tool | Old version | New version |
+| ---- | ----------- | ----------- |
+
+> [!NOTE]
+> Version has been updated if both old and new version information is present.
+> Version has been added if just the new version information is present.
+> Version has been removed if new version information isn't present.
+
 ## 0.5.0 - [2025-03-03]
 
 ### `Added`

assets/multiqc_config.yml

@@ -1,5 +1,5 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/genomic-medicine-sweden/nallo/releases/tag/0.5.0"
+  This report has been generated by the <a href="https://github.com/genomic-medicine-sweden/nallo/tree/dev"
   target="_blank">genomic-medicine-sweden/nallo</a> analysis pipeline.
 report_section_order:
   "genomic-medicine-sweden-nallo-methods-description":

nextflow.config

@@ -345,7 +345,7 @@ manifest {
     mainScript      = 'main.nf'
     defaultBranch   = 'master'
     nextflowVersion = '!>=24.04.2'
-    version         = '0.5.0'
+    version         = '0.6.0dev'
     doi             = '10.5281/zenodo.13748210'
 }
 

ro-crate-metadata.json

@@ -21,8 +21,8 @@
         {
             "@id": "./",
             "@type": "Dataset",
-            "creativeWorkStatus": "Stable",
-            "datePublished": "2025-02-27T12:29:00+00:00",
+            "creativeWorkStatus": "InProgress",
+            "datePublished": "2025-03-03T15:38:02+00:00",
             "description": "[![GitHub Actions CI Status](https://github.com/genomic-medicine-sweden/nallo/actions/workflows/ci.yml/badge.svg)](https://github.com/genomic-medicine-sweden/nallo/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/genomic-medicine-sweden/nallo/actions/workflows/linting.yml/badge.svg)](https://github.com/genomic-medicine-sweden/nallo/actions/workflows/linting.yml)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13748210.svg)](https://doi.org/10.5281/zenodo.13748210)\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\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/genomic-medicine-sweden/nallo)\n\n## Introduction\n\n**genomic-medicine-sweden/nallo** is a bioinformatics analysis pipeline for long-reads from both PacBio and (targeted) ONT-data, focused on rare-disease. Heavily influenced by best-practice pipelines such as [nf-core/sarek](https://nf-co.re/sarek), [nf-core/raredisease](https://nf-co.re/raredisease), [nf-core/nanoseq](https://github.com/nf-core/nanoseq), [PacBio Human WGS Workflow](https://github.com/PacificBiosciences/pb-human-wgs-workflow-snakemake), [epi2me-labs/wf-human-variation](https://github.com/epi2me-labs/wf-human-variation) and [brentp/rare-disease-wf](https://github.com/brentp/rare-disease-wf).\n\n<picture align=\"center\">\n    <img alt=\"genomic-medicine-sweden/nallo workflow\" src=\"docs/images/nallo_metromap.png\">\n  </picture>\n\n## Pipeline summary\n\n##### QC\n\n- Read QC with [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), [cramino](https://github.com/wdecoster/cramino) and [mosdepth](https://github.com/brentp/mosdepth)\n\n##### Alignment & assembly\n\n- Assemble genomes with [hifiasm](https://github.com/chhylp123/hifiasm)\n- Align reads and assemblies to reference with [minimap2](https://github.com/lh3/minimap2)\n\n##### Variant calling\n\n- Call SNVs & joint genotyping with [deepvariant](https://github.com/google/deepvariant) and [GLNexus](https://github.com/dnanexus-rnd/GLnexus)\n- Call SVs with [Severus](https://github.com/KolmogorovLab/Severus) or [Sniffles](https://github.com/fritzsedlazeck/Sniffles)\n- Call CNVs with [HiFiCNV](https://github.com/PacificBiosciences/HiFiCNV)\n- Call tandem repeats with [TRGT](https://github.com/PacificBiosciences/trgt/tree/main) (HiFi only)\n- Call paralogous genes with [Paraphase](https://github.com/PacificBiosciences/paraphase)\n\n##### Phasing and methylation\n\n- Phase and haplotag reads with [LongPhase](https://github.com/twolinin/longphase), [whatshap](https://github.com/whatshap/whatshap) or [HiPhase](https://github.com/PacificBiosciences/HiPhase)\n- Create methylation pileups with [modkit](https://github.com/nanoporetech/modkit)\n\n##### Annotation\n\n- Annotate SNVs and INDELs with databases of choice, e.g. [gnomAD](https://gnomad.broadinstitute.org), [ClinVar](https://www.ncbi.nlm.nih.gov/clinvar/), [CADD](https://cadd.gs.washington.edu) with [echtvar](https://github.com/brentp/echtvar) and [VEP](https://github.com/Ensembl/ensembl-vep)\n- Annotate repeat expansions with [stranger](https://github.com/Clinical-Genomics/stranger)\n- Annotate SVs with [SVDB](https://github.com/J35P312/SVDB) and [VEP](https://github.com/Ensembl/ensembl-vep)\n\n##### Ranking\n\n- Rank SNVs, INDELs, SVs and CNVs with [GENMOD](https://github.com/Clinical-Genomics/genmod)\n\n##### Filtering\n\n- Filter SNVs, INDELs, SVs and CNVs with [filter_vep](https://www.ensembl.org/vep) and [bcftools](https://samtools.github.io/bcftools/bcftools.html)\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\nPrepare a samplesheet with input data:\n\n`samplesheet.csv`\n\n```\nproject,sample,file,family_id,paternal_id,maternal_id,sex,phenotype\nNIST,HG002,/path/to/HG002.fastq.gz,FAM1,HG003,HG004,1,2\nNIST,HG005,/path/to/HG005.bam,FAM1,HG003,HG004,2,1\n```\n\nSupply a reference genome with `--fasta` and choose a matching `--preset` for your data (`revio`, `pacbio`, `ONT_R10`). Now, you can run the pipeline using:\n\n```bash\nnextflow run genomic-medicine-sweden/nallo \\\n    -profile <docker/singularity/.../institute> \\\n    --input samplesheet.csv \\\n    --preset <revio/pacbio/ONT_R10> \\\n    --fasta <reference.fasta> \\\n    --outdir <OUTDIR>\n```\n\nFor more details and further functionality, please refer to the [documentation](http://genomic-medicine-sweden.github.io/nallo/).\n\n## Credits\n\ngenomic-medicine-sweden/nallo was originally written by [Felix Lenner](https://github.com/fellen31).\n\nWe thank the following people for their extensive assistance in the development of this pipeline: [Anders Jemt](https://github.com/jemten), [Annick Renevey](https://github.com/rannick), [Daniel Schmitz](https://github.com/Schmytzi), [Luc\u00eda Pe\u00f1a-P\u00e9rez](https://github.com/Lucpen), [Peter Pruisscher](https://github.com/peterpru) & [Ramprasad Neethiraj](https://github.com/ramprasadn).\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 genomic-medicine-sweden/nallo for your analysis, please cite it using the following doi: [10.5281/zenodo.13748210](https://doi.org/10.5281/zenodo.13748210).\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\nAn extensive list of references for the tools used by the pipeline can be found in the [`docs/CITATIONS.md`](docs/CITATIONS.md) file.\n",
             "hasPart": [
                 {
@@ -102,7 +102,7 @@
             },
             "mentions": [
                 {
-                    "@id": "#4cf45f5c-e791-40f8-a40c-3a173b15005a"
+                    "@id": "#777a47d2-020a-4f42-a191-8e11f56f634a"
                 }
             ],
             "name": "genomic-medicine-sweden/nallo"
@@ -135,7 +135,7 @@
                 }
             ],
             "dateCreated": "",
-            "dateModified": "2025-02-27T12:29:00Z",
+            "dateModified": "2025-03-03T16:38:02Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
             "keywords": [
                 "nf-core",
@@ -160,10 +160,10 @@
             },
             "url": [
                 "https://github.com/genomic-medicine-sweden/nallo",
-                "https://nf-co.re/genomic-medicine-sweden/nallo/0.5.0/"
+                "https://nf-co.re/genomic-medicine-sweden/nallo/dev/"
             ],
             "version": [
-                "0.5.0"
+                "0.6.0dev"
             ]
         },
         {
@@ -179,11 +179,11 @@
             "version": "!>=24.04.2"
         },
         {
-            "@id": "#4cf45f5c-e791-40f8-a40c-3a173b15005a",
+            "@id": "#777a47d2-020a-4f42-a191-8e11f56f634a",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#292f8d16-e2e1-4d21-b520-60aa1f98ee56"
+                    "@id": "#2b8d4522-722f-4739-844a-5861cd8f0148"
                 }
             ],
             "mainEntity": {
@@ -192,7 +192,7 @@
             "name": "Test suite for genomic-medicine-sweden/nallo"
         },
         {
-            "@id": "#292f8d16-e2e1-4d21-b520-60aa1f98ee56",
+            "@id": "#2b8d4522-722f-4739-844a-5861cd8f0148",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing genomic-medicine-sweden/nallo",
             "resource": "repos/genomic-medicine-sweden/nallo/actions/workflows/ci.yml",