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            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-seqsubmit_logo_dark.png\">\n    <img alt=\"nf-core/seqsubmit\" src=\"docs/images/nf-core-seqsubmit_logo_light.png\">\n  </picture>\n</h1>\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/seqsubmit)\n[![GitHub Actions CI Status](https://github.com/nf-core/seqsubmit/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/seqsubmit/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/seqsubmit/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqsubmit/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqsubmit/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\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/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)\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/nf-core/seqsubmit)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqsubmit-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqsubmit)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/seqsubmit** is a Nextflow pipeline for submitting sequence data to [ENA](https://www.ebi.ac.uk/ena/browser/home).\nCurrently, the pipeline supports three submission modes, each routed to a dedicated workflow and requiring its own input samplesheet structure:\n\n- `mags` for Metagenome Assembled Genomes (MAGs) submission with `GENOMESUBMIT` workflow\n- `bins` for bins submission with `GENOMESUBMIT` workflow\n- `metagenomic_assemblies` for assembly submission with `ASSEMBLYSUBMIT` workflow\n\n![seqsubmit workflow diagram](assets/seqsubmit_schema.png)\n\n## Requirements\n\n- [Nextflow](https://www.nextflow.io/) `>=25.04.0`\n- Webin account registered at https://www.ebi.ac.uk/ena/submit/webin/login\n- Raw reads used to assemble contigs submitted to [INSDC](https://www.insdc.org/) and associated accessions available\n\nSetup your environment secrets before running the pipeline:\n\n`nextflow secrets set ENA_WEBIN \"Webin-XXX\"`\n\n`nextflow secrets set ENA_WEBIN_PASSWORD \"XXX\"`\n\nMake sure you update commands above with your authorised credentials.\n\n## Input samplesheets\n\nFor detailed descriptions of all samplesheet columns, see the [usage documentation](docs/usage.md#samplesheet-input).\n\n### `mags` and `bins` modes (`GENOMESUBMIT`)\n\nThe input must follow `assets/schema_input_genome.json`.\n\nRequired columns:\n\n- `sample`\n- `fasta` (must end with `.fa.gz`, `.fasta.gz`, or `.fna.gz`)\n- `accession`\n- `assembly_software`\n- `binning_software`\n- `binning_parameters`\n- `metagenome`\n- `environmental_medium`\n- `broad_environment`\n- `local_environment`\n- `co-assembly`\n\nAt least one of the following must be provided per row:\n\n- reads (`fastq_1`, optional `fastq_2` for paired-end)\n- `genome_coverage`\n\nAdditional supported columns:\n\n- `stats_generation_software`\n- `completeness`\n- `contamination`\n- `RNA_presence`\n- `NCBI_lineage`\n\nIf `genome_coverage`, `stats_generation_software`, `completeness`, `contamination`, `RNA_presence`, or `NCBI_lineage` are missing, the workflow can calculate or infer them when the required inputs are available.\n\nThose fields are metadata required for the [genome_uploader](https://github.com/EBI-Metagenomics/genome_uploader) package.\n\nExample `samplesheet_genomes.csv`:\n\n```csv\nsample,fasta,accession,fastq_1,fastq_2,assembly_software,binning_software,binning_parameters,stats_generation_software,completeness,contamination,genome_coverage,metagenome,co-assembly,broad_environment,local_environment,environmental_medium,RNA_presence,NCBI_lineage\nlachnospira_eligens,data/bin_lachnospira_eligens.fa.gz,SRR24458089,,,spades_v3.15.5,metabat2_v2.6,default,CheckM2_v1.0.1,61.0,0.21,32.07,sediment metagenome,No,marine,cable_bacteria,marine_sediment,No,d__Bacteria;p__Proteobacteria;s__unclassified_Proteobacteria\n```\n\n> [!IMPORTANT]\n> **Samplesheet column requirements**: All columns shown in the example above must be present in your samplesheet, even if some values are empty. Columns must be in exactly the same order as shown.\n\n### `metagenomic_assemblies` mode (`ASSEMBLYSUBMIT`)\n\nThe input must follow `assets/schema_input_assembly.json`.\n\nRequired columns:\n\n- `sample`\n- `fasta` (must end with `.fa.gz`, `.fasta.gz`, or `.fna.gz`)\n- `run_accession`\n- `assembler`\n- `assembler_version`\n\nAt least one of the following must be provided per row:\n\n- reads (`fastq_1`, optional `fastq_2` for paired-end)\n- `coverage`\n\nIf `coverage` is missing and reads are provided, the workflow calculates average coverage with `coverm`.\n\nExample `samplesheet_assembly.csv`:\n\n```csv\nsample,fasta,fastq_1,fastq_2,coverage,run_accession,assembler,assembler_version\nassembly_1,data/contigs_1.fasta.gz,data/reads_1.fastq.gz,data/reads_2.fastq.gz,,ERR011322,SPAdes,3.15.5\nassembly_2,data/contigs_2.fasta.gz,,,42.7,ERR011323,MEGAHIT,1.2.9\n```\n\n> [!IMPORTANT]\n> **Samplesheet column requirements**: All columns shown in the example above must be present in your samplesheet, even if some values are empty. Columns must be in exactly the same order as shown.\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\n### Submission study\n\nAll data submitted through this pipeline must be associated with an ENA study (project). You can either pass an accession of your existing study via `--submission_study`or provide a metadata file via `--study_metadata` and the pipeline will register the study with ENA before submitting your data.\n\nSee the [usage documentation](docs/usage.md#submission-study) for more details.\n\n### Database setup (`CheckM2` and `CAT_pack`)\n\nThe `mags`/`bins` workflow requires databases for completeness/contamination estimation and taxonomy assignment. See [Usage documentation](usage.md) for details.\n\n### Required parameters:\n\n| Parameter                                  | Description                                                                                                       |\n| ------------------------------------------ | ----------------------------------------------------------------------------------------------------------------- |\n| `--mode`                                   | Type of the data to be submitted. Options: `[mags, bins, metagenomic_assemblies]`                                 |\n| `--input`                                  | Path to the samplesheet describing the data to be submitted                                                       |\n| `--outdir`                                 | Path to the output directory for pipeline results                                                                 |\n| `--submission_study` OR `--study_metadata` | ENA study accession (PRJ/ERP) to submit the data to OR metadata file in JSON/TSV/CSV format to register new study |\n| `--centre_name`                            | Name of the submitter's organisation                                                                              |\n\n### Optional parameters:\n\n| Parameter           | Description                                                                              |\n| ------------------- | ---------------------------------------------------------------------------------------- |\n| `--upload_tpa`      | Flag to control the type of assembly study (third party assembly or not). Default: false |\n| `--test_upload`     | Upload to TEST ENA server instead of LIVE. Default: true                                 |\n| `--webincli_submit` | If set to false, submissions will be validated, but not submitted. Default: true         |\n\nGeneral command template:\n\n```bash\nnextflow run nf-core/seqsubmit \\\n   -profile <docker/singularity/...> \\\n   --mode <mags|bins|metagenomic_assemblies> \\\n   --input <samplesheet.csv> \\\n   --centre_name <your_centre> \\\n   --submission_study <your_study> \\\n   --outdir <outdir>\n```\n\nValidation run (submission to the ENA TEST server) in `mags` mode:\n\n```bash\nnextflow run nf-core/seqsubmit \\\n   -profile docker \\\n   --mode mags \\\n   --input assets/samplesheet_genomes.csv \\\n   --submission_study <your_study> \\\n   --centre_name TEST_CENTER \\\n   --webincli_submit true \\\n   --test_upload true \\\n   --outdir results/validate_mags\n```\n\nValidation run (submission to the ENA TEST server) in `metagenomic_assemblies` mode:\n\n```bash\nnextflow run nf-core/seqsubmit \\\n   -profile docker \\\n   --mode metagenomic_assemblies \\\n   --input assets/samplesheet_assembly.csv \\\n   --submission_study <your_study> \\\n   --centre_name TEST_CENTER \\\n   --webincli_submit true \\\n   --test_upload true \\\n   --outdir results/validate_assemblies\n```\n\nLive submission example:\n\n```bash\nnextflow run nf-core/seqsubmit \\\n   -profile docker \\\n   --mode metagenomic_assemblies \\\n   --input assets/samplesheet_assembly.csv \\\n   --submission_study PRJEB98843 \\\n   --test_upload false \\\n   --webincli_submit true \\\n   --outdir results/live_assembly\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/seqsubmit/usage) and the [parameter documentation](https://nf-co.re/seqsubmit/parameters).\n\n## Pipeline output\n\nKey output locations in `--outdir`:\n\n- `mags/` or `bins/`: genome metadata, manifests, and per-sample submission support files\n- `metagenomic_assemblies/`: assembly metadata CSVs and per-sample coverage files\n- `multiqc/`: MultiQC summary report\n- `pipeline_info/`: execution reports, trace, DAG, and software versions\n\nFor full details, see the [output documentation](https://nf-co.re/seqsubmit/output).\n\n## Credits\n\nnf-core/seqsubmit was originally written by [Martin Beracochea](https://github.com/mberacochea), [Ekaterina Sakharova](https://github.com/KateSakharova), [Sofiia Ochkalova](https://github.com/ochkalova), [Evangelos Karatzas](https://github.com/vagkaratzas).\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 `#seqsubmit` channel](https://nfcore.slack.com/channels/seqsubmit) (you can join with [this invite](https://nf-co.re/join/slack)).\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\n<!-- If you use nf-core/seqsubmit 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\nIf you use this pipeline please make sure to cite all used software.\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> **MGnify: the microbiome sequence data analysis resource in 2023**\n>\n> Richardson L, Allen B, Baldi G, Beracochea M, Bileschi ML, Burdett T, et al.\n>\n> Vol. 51, Nucleic Acids Research. Oxford University Press (OUP); 2022. p. D753\u20139. Available from: http://dx.doi.org/10.1093/nar/gkac1080\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",
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