{"id":21318896,"url":"https://github.com/sydney-informatics-hub/indexreferencefasta-nf","last_synced_at":"2025-03-15T22:15:10.262Z","repository":{"id":107913297,"uuid":"534543976","full_name":"Sydney-Informatics-Hub/IndexReferenceFasta-nf","owner":"Sydney-Informatics-Hub","description":"Create required reference genome index files for WGS data analysis","archived":false,"fork":false,"pushed_at":"2023-08-03T10:25:23.000Z","size":73,"stargazers_count":0,"open_issues_count":1,"forks_count":0,"subscribers_count":7,"default_branch":"main","last_synced_at":"2025-01-22T11:13:18.391Z","etag":null,"topics":["bioinformatics","bwa","docker","fasta","gatk4","genome","genomics","index","nextflow","pipeline","reference-genome","samtools","singularity","workflow"],"latest_commit_sha":null,"homepage":"","language":"Nextflow","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Sydney-Informatics-Hub.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2022-09-09T07:30:47.000Z","updated_at":"2023-01-30T05:34:38.000Z","dependencies_parsed_at":null,"dependency_job_id":"11414e4c-9ffe-4c23-b641-6a4c3702aaa4","html_url":"https://github.com/Sydney-Informatics-Hub/IndexReferenceFasta-nf","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Sydney-Informatics-Hub%2FIndexReferenceFasta-nf","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Sydney-Informatics-Hub%2FIndexReferenceFasta-nf/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Sydney-Informatics-Hub%2FIndexReferenceFasta-nf/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Sydney-Informatics-Hub%2FIndexReferenceFasta-nf/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Sydney-Informatics-Hub","download_url":"https://codeload.github.com/Sydney-Informatics-Hub/IndexReferenceFasta-nf/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":243796741,"owners_count":20349264,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bioinformatics","bwa","docker","fasta","gatk4","genome","genomics","index","nextflow","pipeline","reference-genome","samtools","singularity","workflow"],"created_at":"2024-11-21T19:26:11.284Z","updated_at":"2025-03-15T22:15:10.234Z","avatar_url":"https://github.com/Sydney-Informatics-Hub.png","language":"Nextflow","funding_links":[],"categories":[],"sub_categories":[],"readme":"IndexReferenceFasta-nf\n===========\n\n  - [Description](#description)\n  - [Diagram](#diagram)\n  - [User guide](#user-guide)\n  - [Benchmarking](#benchmarking)\n  - [Workflow summaries](#workflow-summaries)\n      - [Metadata](#metadata)\n      - [Component tools](#component-tools)\n      - [Required (minimum)\n        inputs/parameters](#required-minimum-inputsparameters)\n  - [Additional notes](#additional-notes)\n  - [Help/FAQ/Troubleshooting](#helpfaqtroubleshooting)\n  - [Acknowledgements/citations/credits](#acknowledgementscitationscredits)\n\n---\n\n## Description\nThis is a flexible pipeline for generating common reference genome index files for WGS data analysis. IndexReferenceFasta-nf is a Nextflow (DSL2) pipeline that runs the following tools using either Docker or Singularity to run containerised software for:\n* Samtools faidx\n* BWA index\n* GATK CreateSequenceDictionary \n\n## Diagram\n\u003cp align=\"center\"\u003e \n\u003cimg src=\"https://user-images.githubusercontent.com/73086054/189310509-375fea4f-11fb-41ca-ba52-90760e9a5aa3.png\" width=\"80%\"\u003e\n\u003c/p\u003e \n\n## User guide\n**1. Set up**\n\nClone this repository by running:\n```\ngit clone https://github.com/Sydney-Informatics-Hub/IndexReferenceFasta-nf.git\ncd IndexReferenceFasta-nf\n``` \n\n**2. Generate indexes**  \n\nUsers can specify which index files to create by using the `--bwa`, and/or `--gatk` flags. GATK and BWA indexes are optional, while Samtools is run by default. Run the pipeline with:\n\n```\nnextflow run main.nf --ref /path/to/ref.fasta --bwa --gatk -profile \u003cnimbus/gadi/standard\u003e\n```\n\nIf you are running the pipeline on NCI Gadi or Pawsey's Nimbus cloud you should specify this with the `-profile` flag at runtime. This will allow you to use Singularity to run containers at Gadi and Docker to run the containers at Nimbus. \n\n**Standard**\n\nTo run the pipeline on your own system, you will need to have Nextflow installed. You can adjust the `standard.config`  configuration file depending on your own system needs. Currently it runs containers with Singularity. You can test your customised config file using the test fasta available in `testData`.\n\nTo run the pipeline with the `standard.config`, run the following: \n\n```\nnextflow run main.nf --ref /path/to/ref.fasta --bwa --gatk -profile standard \n```\n\n**NCI Gadi HPC**  \n\nTo run the pipeline at NCI Gadi, first load the Gadi-specific Nextflow installation:\n\n```\nmodule load nextflow\n```\n\nThen run the pipeline:\n```\nnextflow run main.nf --ref /path/to/ref.fasta --bwa --gatk -profile gadi --whoami \u003cus1111\u003e --pbs_account \u003caa00\u003e\n``` \n\n**Pawsey Nimbus cloud**\n\nTo run the pipeline at Pawsey's Nimbus cloud:\n\n```\nnextflow run main.nf --ref /path/to/ref.fasta --bwa --gatk -profile nimbus\n```\n\nInfrasturcture-specific config files can be found in `config/`\n\n## Benchmarking\n\n### Human hg38 reference assembly @ Pawsey's Nimbus (NCPU/task = 1)\n|task_id|hash     |native_id|name          |status   |exit|submit |duration  |realtime  |%cpu   |peak_rss|peak_vmem|rchar  |wchar  |\n|-------|---------|---------|--------------|---------|----|-------|----------|----------|-------|--------|---------|-------|-------|\n|3      |27/33fffc|131621   |samtools_index|COMPLETED|0   |55:44.9|12.2s     |12s       |99.20% |6.3 MB  |11.8 MB  |3 GB   |19.1 KB|\n|1      |80/f03e46|131999   |gatk_index    |COMPLETED|0   |55:46.7|22.6s     |22.3s     |231.90%|3.8 GB  |37.1 GB  |3.1 GB |726 KB |\n|2      |ea/e29535|131594   |bwa_index     |COMPLETED|0   |55:44.9|1h 50m 16s|1h 50m 15s|99.50% |4.5 GB  |4.5 GB   |12.1 GB|8.2 GB |\n\n## Workflow summaries\n\n### Metadata\n|metadata field     | workflow_name / workflow_version  |\n|-------------------|:---------------------------------:|\n|Version            | 1.0                               |\n|Maturity           | stable\t\t                |\n|Creators           | Georgie Samaha                    |\n|Source             | NA                                |\n|License            | GPL-3.0 license                   |\n|Workflow manager   | NextFlow                          |\n|Container          | None                              |\n|Install method     | NA                            |\n|GitHub             | Sydney-Informatics-Hub/IndexReferenceFasta-nf                                |\n|bio.tools          | NA                                |\n|BioContainers      | NA                                | \n|bioconda           | NA                                |\n\n### Component tools\n\n* samtools/1.15.1\n* gatk/4.3.0.0 \n* bwa/0.7.17\n\n### Required (minimum) inputs/parameters\n\n* A reference genome file in fasta format.\n\n## Additional notes\n\n### Help/FAQ/Troubleshooting\n\n* A subset fasta file for testing is available in [`testData/`](https://github.com/Sydney-Informatics-Hub/IndexReferenceFasta-nf/tree/main/testData) \n\n## Acknowledgements/citations/credits\n### Authors \n- Georgie Samaha (Sydney Informatics Hub, University of Sydney)   \n\n### Acknowledgements \n\n- This pipeline was built using the [Nextflow DSL2 template](https://github.com/Sydney-Informatics-Hub/Nextflow_DSL2_template).  \n- Documentation was created following the [Australian BioCommons documentation guidelines](https://github.com/AustralianBioCommons/doc_guidelines).  \n\n### Cite us to support us! \nAcknowledgements (and co-authorship, where appropriate) are an important way for us to demonstrate the value we bring to your research. Your research outcomes are vital for ongoing funding of the Sydney Informatics Hub and national compute facilities. We suggest including the following acknowledgement in any publications that follow from this work:  \n\nThe authors acknowledge the technical assistance provided by the Sydney Informatics Hub, a Core Research Facility of the University of Sydney and the Australian BioCommons which is enabled by NCRIS via Bioplatforms Australia. \n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsydney-informatics-hub%2Findexreferencefasta-nf","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsydney-informatics-hub%2Findexreferencefasta-nf","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsydney-informatics-hub%2Findexreferencefasta-nf/lists"}