separate rule for singletons

ktmeaton · Aug 25, 2021 · c4b8ba5 · c4b8ba5
1 parent 35e6aab
commit c4b8ba5
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Showing 2 changed files with 9 additions and 17 deletions.
diff --git a/workflow/rules/qc.smk b/workflow/rules/qc.smk
@@ -228,7 +228,7 @@ rule variant_qc:
         # het
         header="$header\t"`head -n 1 {input.het_files[0]} | sed 's/sample\t//g'`;
         # singletons
-        header="$header\t"`head -n 1 {input.singletons[0]} | sed 's/sample\t//g'`;
+        header="$header\t"`head -n 1 {input.singletons} | sed 's/sample\t//g'`;
         echo -e $header > {output.df};
 
         for file in {input.tstv_files};

diff --git a/workflow/rules/targets.smk b/workflow/rules/targets.smk
@@ -69,26 +69,18 @@ rule snippy_pairwise_local:
 # Locus Coverage
 #------------------------------------------------------------------------------#
 
-locus_coverage_collect_all_input = results_dir + "/locus_coverage_collect/all/locus_coverage.txt"
-locus_coverage_collect_local_input    = locus_coverage_collect_all_input.replace("all", "local")
-locus_coverage_collect_assembly_input    = locus_coverage_collect_all_input.replace("all", "assembly")
-locus_coverage_collect_sra_input    = locus_coverage_collect_all_input.replace("all", "sra")
+locus_coverage_collect_all_input        = results_dir + "/locus_coverage_collect/all/locus_coverage.txt"
+locus_coverage_collect_local_input      = locus_coverage_collect_all_input.replace("all", "local")
+locus_coverage_collect_assembly_input   = locus_coverage_collect_all_input.replace("all", "assembly")
+locus_coverage_collect_sra_input        = locus_coverage_collect_all_input.replace("all", "sra")
 
-rule locus_coverage_collect_all:
-    input:
-        locus_coverage_collect_all_input
+rule locus_coverage_collect_all:        input: locus_coverage_collect_all_input
 
-rule locus_coverage_collect_assembly:
-    input:
-        locus_coverage_collect_assembly_input
+rule locus_coverage_collect_assembly:   input: locus_coverage_collect_assembly_input
 
-rule locus_coverage_collect_sra:
-    input:
-        locus_coverage_collect_sra_input,
+rule locus_coverage_collect_sra:        input: locus_coverage_collect_sra_input,
 
-rule locus_coverage_collect_local:
-    input:
-        locus_coverage_collect_local_input
+rule locus_coverage_collect_local:      input: locus_coverage_collect_local_input
 
 #------------------------------------------------------------------------------#
 # Singletons