order log changes

Author: pdimens

rules/LepMap3/order.smk

@@ -2,9 +2,10 @@ rule order_markers:
     input:
         datacall = "2_Filtering/data.filtered.lepmap3.gz",
         filt_map = "LOD.master"
-    output: "4_OrderMarkers/ordered.{lg_range}"
+    output: 
+        lg = "4_OrderMarkers/ordered.{lg_range}",
+        runlog = temp("4_OrderMarkers/logs/ordered.{lg_range}.running")
     log:
-        runlog = temp("4_OrderMarkers/logs/ordered.{lg_range}.running"),
         run = "4_OrderMarkers/logs/ordered.{lg_range}.log",
         recomb = "4_OrderMarkers/recombination/ordered.{lg_range}.recombinations"
     message: "Ordering linkage group {params.chrom} with {params.iterations} iterations"
@@ -15,10 +16,10 @@ rule order_markers:
     threads: 2
     shell:
         """
-        zcat {input.datacall} | java -cp software/LepMap3 OrderMarkers2 map={input.filt_map} {params.extra} data=- numThreads={threads} numMergeIterations={params.iterations} chromosome={params.chrom} &> {log.runlog}
-        sed -n '/\*\*\* LG \=/,$p' {log.runlog} > {output}
-        grep "recombin" {log.runlog} > {log.recomb}
-        awk '/#java/{{flag=1}} flag; /logL/{{flag=0}}' {log.runlog} > {log.run}
+        zcat {input.datacall} | java -cp software/LepMap3 OrderMarkers2 map={input.filt_map} {params.extra} data=- numThreads={threads} numMergeIterations={params.iterations} chromosome={params.chrom} &> {output.runlog}
+        sed -n '/\*\*\* LG \=/,$p' {output.runlog} > {output.lg}
+        grep "recombin" {output.runlog} > {log.recomb}
+        awk '/#java/{{flag=1}} flag; /logL/{{flag=0}}' {output.runlog} > {log.run}
         """
 
 rule recomb_summary:

rules/LepMap3/reorder.smk

@@ -3,9 +3,10 @@ rule reorder_markers:
         datacall = "2_Filtering/data.filtered.lepmap3.gz",
         filt_map = "LOD.master",
         lg_order = "5_Trim/ordered.{lg_range}.trimmed"
-    output: "6_OrderMarkers/ordered.{lg_range}"
+    output: 
+        lg = "6_OrderMarkers/ordered.{lg_range}",
+        runlog = temp("6_OrderMarkers/logs/ordered.{lg_range}.running")
     log:
-        runlog = temp("6_OrderMarkers/logs/ordered.{lg_range}.running"),
         run = "6_OrderMarkers/logs/ordered.{lg_range}.log",
         recomb = "6_OrderMarkers/recombination/ordered.{lg_range}.recombination"
     message: "Reordering linkage group {params.lg} with {params.iterations} iterations"
@@ -16,10 +17,10 @@ rule reorder_markers:
     threads: 2
     shell:
         """
-        zcat {input.datacall} | java -cp software/LepMap3 OrderMarkers2 {params.extra} map={input.filt_map} data=- numThreads={threads} evaluateOrder={input.lg_order} numMergeIterations={params.iterations} &> {log.runlog}
-        sed -n '/\*\*\* LG \=/,$p' {log.runlog} > {output}
-        grep "recombin" {log.runlog} > {log.recomb}
-        awk '/#java/{{flag=1}} flag; /logL/{{flag=0}}' {log.runlog} > {log.run}
+        zcat {input.datacall} | java -cp software/LepMap3 OrderMarkers2 {params.extra} map={input.filt_map} data=- numThreads={threads} evaluateOrder={input.lg_order} numMergeIterations={params.iterations} &> {output.runlog}
+        sed -n '/\*\*\* LG \=/,$p' {output.runlog} > {output.lg}
+        grep "recombin" {output.runlog} > {log.recomb}
+        awk '/#java/{{flag=1}} flag; /logL/{{flag=0}}' {output.runlog} > {log.run}
         """
 
 rule reorder_summary: