- header: Quick Instruction
  text:
    - >-
      Fill the sheets in the order that they appear (apart from Collaborators,
      Repositories, Extra Attributes, see appropriate entry).
    - >-
      Fields marked with * are mandatory
      - >-
      Do not delete rows and columns that you don't fill in, just leave them
      empty
    - >-
      Values for fields with red triangle in the corner need to be chosen from
      available values
    - >-
      Fields with light green background accept multiple values separated
      by ; (semicolon)
    - >-
      Fields with light blue background can be present in the table multiple
      times and can be copied and pasted on the rows below if necessary
    - >-
      Fill in the Samples and Runs by copying the first empty row below, this
      will preserve the fields where you need to choose multiple values
    - >-
      For Studies, Experiments and Datasets, if multiple tables are needed,
      copy the whole table to the right (see image below)
- header: Aliases (Placeholders)
  text:
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      It is used to create placeholder IDs that links your Samples, Experiments,
      Runs, Analyses and Datasets internally. These placeholder IDs will be
      translated to provisional or accession IDs during submission. Complete
      this sheet first, assigning a unique placeholder ID for each Sample,
      Experiment, Run, Analysis (if available) and Dataset.
    - >-
      Placeholders for
      Samples will become the sample names. You may choose any name (e.g.
      Sample1, Sample2, …), but it must be unique across all submissions
      under the same EGA account.
    - >-
      This sheet is not a rectangular dataframe. It is simply a list of
      individual items. See the `Aliases` sheet for
      an example.
- header: Files
  text:
    - >-
      Names of all raw files for the submission.  If files are encrypted and
      differ only by the `.c4gh` extension, do not include the extension.
      It will be added automatically during submission.
    - >-
      Do not prefix the file names with slashes or other relative paths.
    - >-
      If the files are located in a sub-directory within your `encrypted`
      EGA Inbox, specify the name of the sub-directory in the
      'EGA Inbox Relative Path' name column.
    - >-
      Complete this sheet after the Aliases sheet, as other sheets depend on it.
- header: Analysis Files
  text:
    - >-
      Names of all raw files for the submission.  If files are encrypted and
      differ only by the `.c4gh` extension, do not include the extension.
      It will be added automatically during submission.
    - >-
      Do not prefix the file names with slashes or other relative paths.
    - >-
      If the files are located in a sub-directory within your `encrypted`
      EGA Inbox, specify the name of the sub-directory in the
      'EGA Inbox Relative Path' name column.
    - >-
      Complete this sheet after the Aliases sheet, as other sheets depend on it.
    - >-
      If no analyses files are provided, leave the fields empty.
- header: Submission
  text:
    - >-
      The top level item that encompasses all the other and will receive an
      Accession ID for tracking. This name and description will only be used
      internally during the submission process and will not be visible on the
      EGA webpage. For referencing in your manuscript you will only use the
      Study ID or the Dataset ID.
- header: Studies
  text:
    - >-
      Title is expected to be between 3 to 20 words. The title of the studies
      doesn’t need to match the EGA submission name.
    - >-
      Provide a 3-5 sentences as description with background, goals,
      and key details. One submission can include one or more studies.
- header: Samples
  text:
    - >-
      List all biological samples. Duplicate the row to add additional samples.
      Each Subject ID must be linked to a Sample Alias to link files to samples.
    - >-
      Try to make the Sample names/aliases unique to not interfere with other
      submissions.
- header: Experiments
  text:
    - >-
      Specify how the experiment was performed (e.g., instrument model, design
      name, library type) You can create more experiments if you have different
      data types in the same study/EGA submission (e.g. ATAC-seq and RNA-seq).
- header: Runs
  text:
    - >-
      Runs connect samples to files and experiment. Duplicate the first row to
      add more runs. Files cannot be reused among the different Runs. Each file
      can only be associated to one Run.
- header: Analyses
  text:
    - >-
      Analyses gather processed files, for example BAM or VCF files including
      mapping info. They are linked to one study and to one/multiple samples,
      files and experiments.
    - >-
      Currently this is the only sheet/entry that is optional for the EGA
      submission. If you don't want to submit any analyses, delete the entries
      in the Alias sheet. There is not need to delete 'Analysis Files' and
      'Analyses' sheets, you can leave them empty.
    - >-
      Analysis files cannot be reused among the different Analyses
    - >-
      There are three types of analyses: REFERENCE ALIGNMENT, SEQUENCE VARIATION
      and SAMPLE PHENOTYPE and they have specific requirements for which other
      fields must or cannot be specified. See the entry at the end of the
      Instructions sheet for details.
- header: Datasets
  text:
    - >-
      For each dataset, you need to a Policy Accesion ID, this will be usually
      issued by your institution or a commitee that controls data access.
    - >-
      Title is expected to be between 3 to 20 words.
    - >-
      Description is expected to be a 3-4 sentences
      (at least 50 characters), definition of the dataset content, including
      sample number and details, file type, and technology/experimentation used.
- header: Collaborators, Repositories, Extra Attributes
  text:
    - >-
      These fields are present in other sheets, but for submission they are
      formatted as key value pairs.
    - >-
      If you wish to add any of these to your submission, please create an
      appropriate entry in one of these 3 sheets and you will be able to select
      in from a dropdown menu afterwards.

- header: Additional requirements for Analyses sheet
  text:
    - >-
      REFERENCE ALIGNMENT Analysis type must have 'Experiment Types', 'Genome ID',
      'Chromosomes groups' or 'Chromosomes' specified
    - >-
      SEQUENCE VARIATION Analysis type must have 'Experiment Types', 'Genome ID',
      'Chromosomes groups' or 'Chromosomes' specified
    - >-
      SAMPLE PHENOTYPE Analysis type cannot have 'Experiment Types', 'Platform',
      'Genome ID', 'Chromosome groups' and 'Chromosomes' specified
    - >-
      Selected 'Chromosome groups' and 'Chromosomes' must match 'Genome ID'
