fix paired rule

linsalrob · Jul 26, 2024 · 95b317a · 95b317a
1 parent d3496a0
commit 95b317a
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/sphae/workflow/rules/10.final-reporting.smk b/sphae/workflow/rules/10.final-reporting.smk
@@ -75,7 +75,7 @@ rule summarize_paired:
         table= os.path.join(dir_genome, "{sample}-pr", "{sample}-genome-candidates.csv"),
         genome=os.path.join(dir_genome, "{sample}-pr", "{sample}.fasta"),
         gbk=os.path.join(dir_annotate, "phynteny-pr", "{sample}_1_phynteny", "phynteny.gbk"),
-        plot=os.path.join(dir_annotate, "phynteny-sr", "{sample}_1_phynteny", "plots", "{sample}_1.png"),
+        plot=os.path.join(dir_annotate, "phynteny-pr", "{sample}_1_phynteny", "plots", "{sample}_1.png"),
         ph_taxa=os.path.join(dir_annotate, "pharokka-pr", "{sample}_1_pharokka", "{sample}_1_top_hits_mash_inphared.tsv"),
         cdden=os.path.join(dir_annotate, "pharokka-pr", "{sample}_1_pharokka", "{sample}_1_length_gc_cds_density.tsv"),
         cds=os.path.join(dir_annotate, "pharokka-pr", "{sample}_1_pharokka", "{sample}_1_cds_functions.tsv"),

diff --git a/sphae/workflow/rules/9.phynteny.smk b/sphae/workflow/rules/9.phynteny.smk
@@ -43,7 +43,7 @@ rule phynteny_plotter_paired:
         inputdir=os.path.join(dir_annotate, "{sample}-pr-genomes"),
         idir=os.path.join(dir_annotate, "phynteny-pr"), 
     output:
-        plot=os.path.join(dir_annotate, "phynteny-pr", "{sample}_1_phynteny", "pharokka_plot.png")
+        plot=os.path.join(dir_annotate, "phynteny-pr", "{sample}_1_phynteny", "plots", "{sample}_1.png")
     resources:
         mem =config['resources']['smalljob']['mem'],
         time = config['resources']['smalljob']['time']