S3C-SIS-TASK-11: Consensus sequences need to be manually imported.

[uweschmitt]

Relates to issue https://gitlab.ethz.ch/sars_cov_2/s3c-it-tasks/-/issues/11

• I forked from rubicon branch since this was the branch I found on euler
• I tried to extend V-pipe to collect the consensus sequences at the end of each run and to compute/determine for the sequences:
  • batch / sample id (based on path) of ref_ambig_dels.fasta
  • creation time stamp of ref_ambig_dels.fasta
  • seguid and crc64 checksum for each sequence in ref_ambig_dels.fasta.

The rule finally writes a file summary.json to the current working directory.

This is an initial attempt replace the manually triggered import script without coupling V-pipe to the infrastructure of the overall S3C workflow.

This pull request is accompanied by https://github.com/cbg-ethz/pangolin/pull/3 which includes a script to read the created summary.json file and uploads it to the S3C database.

Future work will be to complete the information in summary.json.

[uweschmitt]

superseded by https://github.com/cbg-ethz/V-pipe/pull/116