Co-assemblies submission support with mode "mags/bins" and "metagenomic_assemblies"

[KateSakharova]

Description of feature

assembly-uploader supports co-assemblies. We need to modify assemblysubmit schema to recieve a list of runs

[ochkalova]

Approximate list of changes to make this possible (hardest case: no coverage provided in the input, no virtual sample is submitted)

• Modify schemas assets/schema_input_genome.json and assets/schema_input_assembly.json to accept multiple runs.

ASSEMBLYSUBMIT:

• Modify meta construction from samplesheet to allow for multiple runs.
• Make sure COVERM_CONTIG can accept multiple runs.
• Modify average coverage calculation (file format of COVERM_CONTIG will change)
• Update CREATE_ASSEMBLY_METADATA_CSV module
• Implement umbrella sample generation in assembly_uploader tool

GENOMESUBMIT:

• Modify meta construction from samplesheet to allow for multiple runs.
• Make sure COVERM_GENOME can accept multiple reads
• Modify average coverage calculation (file format of COVERM_CONTIG will change)
• Update CREATE_GENOME_METADATA_TSV module
• Make sure genome-uploader can use umbrella samples (should be done by @ochkalova)