Submitting a metagenome assembly
==================

The submission of the assembly can be done only using ``webin-cli``.

Again, We will need to create a manifest file, which contains the metadata for our read data and references the assembly ``fasta`` file that should be submitted.

First, we create another directory::

  mkdir /mnt/submission/assembly/assembly

Then, we ``gzip`` the assembly file, since it needs to be zipped for submission::
  
  gzip /mnt/WGS-data/megahit_out/final.contigs.fa
  
And change to our submission directory::
  
  cd /mnt/submission/assembly/assembly

Create the manifest file
^^^^^^^^^^

We will use this short manifest template for our submission, fill in YOUR values for STUDY, SAMPLE and RUN accession and provide an assembly name as well as the assembly result fasta file::

  STUDY   TODO
  SAMPLE   TODO
  RUN_REF   TODO
  ASSEMBLYNAME   TODO
  ASSEMBLY_TYPE   primary metagenome
  COVERAGE   20
  PROGRAM   MEGAHIT
  PLATFORM   ILLUMINA
  MOLECULETYPE   genomic DNA
  DESCRIPTION   MEGAHIT assembly of the MG course 2024 dataset
  FASTA   TODO
  
Create a file named ``manifest`` and fill it with the content above - fill the fields marked with TODO with the appropriate content. Then continue with the next step.

Validating the assembly submission
^^^^^^^^^^^^^^^^^^

Before actually submitting, we are validating our manifest file. To do so, we use the option ``-validate`` in our call of ``webin-cli``. Also, make sure, to use the ``-test`` flag to submit to the ENA test server. We also use ``-context=genome`` since we are submitting an assembly. Other options are your ``-username``, ``-password`` and the path to the ``-manifest`` file::
  
  cd /mnt/submission/assembly/assembly
  java -jar ~/webin-cli-6.10.0.jar -username=$ENA_USER -password=$ENA_PWD -context=genome -manifest=manifest -validate -test

When everything was successfully validated, you should get a message like::

  INFO : The submission has been validated successfully.


Submit the assembly
^^^^^^^^^^^^^^^^

Now, that our assembly submission is validated successfully, we can go on with the submission. Just replace the ``-validate`` flag by ``-submit`` in the ``webin-cli`` call. Do NOT remove the ``-test`` flag::

  cd /mnt/submission/assembly/assembly
  java -jar  ~/webin-cli-6.10.0.jar -username=$ENA_USER -password=$ENA_PWD -context=genome -manifest=manifest -submit -test
 
If everything works fine, you should receive a message like::

  INFO : The TEST submission has been completed successfully. This was a TEST submission and no data was submitted. The following analysis accession was assigned to the submission: ERZ14243535

Great! Now let's go on by adding bins and MAGs to this assembly.


References
^^^^^^^^^^
**ENA - Submitting A Primary Metagenome Assembly** https://ena-docs.readthedocs.io/en/latest/submit/assembly/metagenome/primary.html