Monster PR

[priesgo]

Changes

• Fix parsing of host from COVID19 Data Portal
• Avoid writing config in logs multiple times
• Change in COVID19 Data Portal from acc to id
• Add binary search on existing sample ids to improve accessor performance
• Infinite retries on accessor
• Skip pangolin for COVID19 Data Portal and use provided pangolin
• Update use of COVID19 Data Portal to query by montsh to avoid limitation in the maximum number of results
• Avoid erroring if the API returns repeated samples...
• Add an option to run pipeline directly from VCF for rephasing
• Integrate COMPLLEX mutations
• Enable configuration of nextflow profile instead of using conda always. By default still uses conda profile