S3c sis task 7 and 11

[uweschmitt]

Relates to https://gitlab.ethz.ch/sars_cov_2/s3c-it-tasks/-/issues/7 and 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.

• I rewrote the existing dehuman.bsub as a rule.

• the workflow now generates a file summary.zip which includes the consensus sequence information in a file summary.zip plus the dehuman.cram files for each data set.

• must be enabled in config file

• path humane genome .fa file must be configured also

[uweschmitt]

@DrYak Please check https://github.com/cbg-ethz/V-pipe/pull/116/commits/93afb8bf23e6bf1a8715a839847dd026ed106feb I replaced the upload strategy by setting up an uploads folder with symbolic links as discussed.

[DrYak]

Into production now as of 066dcbdd3c9da8ab694ab4d8713c5ff9baab4437