p3-submit-sars2-analysis

Submit a PATRIC SARS-CoV-2 Analysis Job

p3-submit-sars2-analysis [options] output-path output-name

Submit a set of one or more read libraries to the PATRIC SARS-CoV-2 assembly service.

Usage synopsis

p3-submit-sars2-analysis [-h] output-path output-name

   Submit an assembly job with output written to output-path and named
   output-name.

   The following options describe the inputs to the assembly:

       --workspace-path-prefix STR   Prefix for workspace pathnames as given
                                    to library parameters.
       --workspace-upload-path STR  If local pathnames are given as library parameters,
                                    upload the
                                    files to this directory in the workspace.
       --overwrite                  If a file to be uploaded already exists in
                                    the workspace, overwrite it on upload. Otherwise
                                    we will not continue the service submission.
      --paired-end-lib P1 P2        A paired end read library. May be repeated.
       --single-end-lib LIB                 A single end read library. May be repeated.
      --srr-id STR                  Sequence Read Archive Run ID. May be repeated.

   The following options describe the processing requested:

              --scientific-name STR         Scientific name for this genome.
       --taxonomy-id STR            Taxonomy id for this genome.
       --recipe                      Assembly recipe. Defaults to auto.
                                    Valid values are cdc-nanopore, cdc-illumina, or artic-nanopore
       --container-id               (Internal) Use the specified container to run this application

The following options describe the read libraries:

       --platform STR               The sequencing platform for the next read
                                    library or libraries. Valid values are
                                    infer, illumina, pacbio, nanopore, iontorrent