Update automation logic when metagenome workflow process starts from annotation

[aclum]

IMG is having issues ingesting our re-annotation of JGI assemblies b/c the contigs are named based on JGI assembly group (scaffold_1_c1) and the annotation files use nmdc naming convention without a conversion file (nmdc:wfmgan-11-2r9bkx60.1_1_c1)
example omics processing directory nmdc:omprc-11-14ermv40

I believe this can be fixed by specifying pre_qc_execute=true to the structural-annotation.wdl. I'm making a related ticket in the mg_annotation repo to make sure this works correctly. Automation code will need to make a mongo record for the mapping file (*_contig_names_mapping.tsv). This file already has an enumeration in the schema 'Contig Mapping File'. That mapping file then needs to be passed to the MAGs workflow.

acceptance criteria:

From a workflow run starting with a JGI assembly as input, there is a directory on the file system which contains a mapping file with extension _contig_names_mapping.tsv with a corresponding DataObject mongo with data_object_type of Contig Mapping File. That mapping file is correctly passed to MagsAnalysisActivity and that activity completes successfully.

[aclum]

@Michal-Babins made a good point that this should only apply if the assembly was not generated by NMDC. You could look at processing_institution for the assembly component for the logic statement.

[aclum]

backlogging this in favor of issues #54 and re-iding work.

[aclum]

@chienchi can you make a new release of metaMAGs with the fixes to provide the mapping file so the automation logic can test updating to using that version to optionally supply a mapping file.

[aclum]

Chienchi made a new release for metagenomes, we are still blocked on microbiomedata/mg_annotation#24

[aclum]

Duplicate of #191