This PR adds an output to both TheiaProk workflows containing a fasta file of novel MLST allele sequences.
In task_ts_mlst.wdl, I added a --novel flag to the mlst command, and output the results, ~{samplename}_novel_mlst_alleles.fasta in a new column, ts_mlst_novel_alleles
Theiaprok PE and SE wf’s and task_broad_terra_tools.wdl have had the new output column added
I have tested the task on the command line, and tested the PE and SE workflows on Terra, using both inputs that include novel alleles and those that do not. All tests have been successful.
This PR adds an output to both TheiaProk workflows containing a fasta file of novel MLST allele sequences.
task_ts_mlst.wdl, I added a--novelflag to the mlst command, and output the results,~{samplename}_novel_mlst_alleles.fastain a new column,ts_mlst_novel_allelestask_broad_terra_tools.wdlhave had the new output column addedI have tested the task on the command line, and tested the PE and SE workflows on Terra, using both inputs that include novel alleles and those that do not. All tests have been successful.