smll fix

Changes.md

@@ -8,10 +8,11 @@
 - Updating the QC rule to touch the output file so the error is correctly recorded
 - the annotate function table after the 3Ps werent being generated, so added that in
 - add the number of unknown proteins to the final summary file
-- updated phytnteny yaml file to include numpy version
+- updated phynteny yaml file to include numpy version
 - added a python script to the misc folder to merge the RESULTS to one tsv file
 - adding the total read length to summary file
 - updating the taxa description in the summary file to include the taxa description, lowest taxa and the isolated host from the pharokka inphared result
+- added the --no-polish option
 
 
 ## v1.4.2 

sphae/config/config.yaml

@@ -9,6 +9,7 @@ resources:
     time: 480
 
 params:
+  no_medaka: False
   medaka: "r1041_e82_400bps_sup_v4.2.0" # the current default in medaka v1.8 and the most recent model
   flye: "--nano-hq"
   genomeSize: 44k 

sphae/workflow/rules/9.phynteny.smk

@@ -48,14 +48,14 @@ rule phynteny_plotter_paired:
         mem =config['resources']['smalljob']['mem'],
         time = config['resources']['smalljob']['time']
     conda:
-        os.path.join(dir_env, "pharokka.yaml")
+        os.path.join(dir_env, "phold.yaml")
     shell:
         """
         if [[ -s {input.gbk} ]] ; then
             for f in {params.inputdir}/*; do 
                 data="$(basename "$f" .fasta)"
                 genbank_to -g {params.idir}/"$data"_phynteny/phynteny.gbk --gff3 {params.idir}/"$data"_phynteny/phynteny.gff3
-                phold plot -i {params.idir}/"$data"_phynteny/phynteny.gbk -f -p "$data"_phynteny -o {params.idir}/"$data"_phynteny           
+                phold plot -i {params.idir}/"$data"_phynteny/phynteny.gbk -f -o {params.idir}/"$data"_phynteny/plots    
             done
             touch {output.plot}
         else