S3c sis task 7 and 11 #116
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This was referenced Dec 14, 2021
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Into production now as of 066dcbd |
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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
rubiconbranch since this was the branch I found on eulerI 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 ofref_ambig_dels.fastaseguid 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