Feature/studysubmit #36

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Merged

ochkalova merged 38 commits into dev from feature/studysubmit

Mar 25, 2026

README.md

            
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    @@ -116,15 +116,21 @@ assembly_2,data/contigs_2.fasta.gz,,,42.7,ERR011323,MEGAHIT,1.2.9
  
    > [!NOTE]

    > 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.

    ### Submission study

    All 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.

    See the [usage documentation](docs/usage.md#submission-study) for more details.

    ### Required parameters:

    | Parameter            | Description                                                                       |

    | -------------------- | --------------------------------------------------------------------------------- |

    | `--mode`             | Type of the data to be submitted. Options: `[mags, bins, metagenomic_assemblies]` |

    | `--input`            | Path to the samplesheet describing the data to be submitted                       |

    | `--outdir`           | Path to the output directory for pipeline results                                 |

    | `--submission_study` | ENA study accession (PRJ/ERP) to submit the data to                               |

    | `--centre_name`      | Name of the submitter's organisation                                              |

    | Parameter                                  | Description                                                                                                       |

    | ------------------------------------------ | ----------------------------------------------------------------------------------------------------------------- |

    | `--mode`                                   | Type of the data to be submitted. Options: `[mags, bins, metagenomic_assemblies]`                                 |

    | `--input`                                  | Path to the samplesheet describing the data to be submitted                                                       |

    | `--outdir`                                 | Path to the output directory for pipeline results                                                                 |

    | `--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 |

    | `--centre_name`                            | Name of the submitter's organisation                                                                              |

    ### Optional parameters:

assets/study_metadata.json

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+    {
+        "alias": "study-example-2026",
+        "study_title": "Example metagenome study",
+        "study_abstract": "Description of the study aims and methods.",
+        "existing_study_type": "Metagenomics"
+    }

assets/study_metadata.tsv

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		alias study_title study_abstract existing_study_type
		study-example-2026 Example metagenome study Description of the study aims and methods. Metagenomics

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