Unicyler refactoring kao Clade I Rewrite #27
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…hanges related to making the gfa script able to handle clade I, also added the same logging and summary file present in the original script, but a lot of the script was reorganized and refactored
… comments, added proper spacing, fixed author atribution
…de in the itr for segment order/orientation, 2- updated graph recon submodule and subworkflows to properly name log and summary outputs and pass all channels correctly downstream, 3- fixed summarize qc to align the script with the new format of the log file coming out of graph recon, and to modified the kraken db variable to fix some bug where it wasnt grabbing the kraken-db within the function and writing to final outfile
This PR is against the
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@mikeyweigand I will send the testing commands offline. |
…TRs to be double the target length
…f the ITRs. The new version keeps all longest paths, determines the orientations of all paths in the list, then uses quast to find the best alignment with the reference and keep that longest path as the final path under the assumption that the wrongly oriented path will align more poorly."
…updated get_final_orientation function
…s, then selects conneected itrs based on list with terminal itr in it, if there are no connected itrs, then there is 1 itr contig, the terminal itr.
…e case of one long contig and only an ITR, as well as handle broken (non cyclical) sequences
…e find final orientation step, now it removes those contigs / edges from the links before walking the path to find the orientation of each contig
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