swap order for ordering function call (top/htop convenience)

pdimens · Feb 3, 2022 · 6e3c698 · 6e3c698
1 parent ddb5730
commit 6e3c698
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Showing 3 changed files with 4 additions and 4 deletions.
diff --git a/rules/LepMap3/distances.smk b/rules/LepMap3/distances.smk
@@ -19,10 +19,10 @@ rule calculate_distances:
         """
         cp {input.lg} {output.distance}
         
-        zcat {input.data_call} | java -cp software/LepMap3 OrderMarkers2 data=- evaluateOrder={input.lg} {params.dist_method} numThreads={threads} improveOrder=0 sexAveraged=1 &> {output.sex_averagedtmp}
+        zcat {input.data_call} | java -cp software/LepMap3 OrderMarkers2 evaluateOrder={input.lg} data=- {params.dist_method} numThreads={threads} improveOrder=0 sexAveraged=1 &> {output.sex_averagedtmp}
         sed -i -e 's/LG \= 0/LG \= {params.lg}/g' {output.sex_averagedtmp}
         sed -n '/\*\*\* LG \=/,$p' {output.sex_averagedtmp} > {output.sex_averaged} 
         awk '/#java/{{flag=1}} flag; /*** LG =/{{flag=0}}' {output.sex_averagedtmp} > {log.sex_averaged}
 
-        zcat {input.data_call} | java -cp software/LepMap3 OrderMarkers2 data=- evaluateOrder={input.lg} {params.dist_method} numThreads={threads} calculateIntervals={output.intervals} > {log.intervals} 2>&1
+        zcat {input.data_call} | java -cp software/LepMap3 OrderMarkers2 evaluateOrder={input.lg} data=- {params.dist_method} numThreads={threads} calculateIntervals={output.intervals} > {log.intervals} 2>&1
         """
diff --git a/rules/LepMap3/order.smk b/rules/LepMap3/order.smk
@@ -15,7 +15,7 @@ rule order_markers:
     threads: 2
     shell:
         """
-        zcat {input.datacall} | java -cp software/LepMap3 OrderMarkers2 map={input.filt_map} {params.extra} data=- numThreads={threads} chromosome={params.chrom} &> {output.runlog}
+        zcat {input.datacall} | java -cp software/LepMap3 OrderMarkers2 chromosome={params.chrom} map={input.filt_map} {params.extra} data=- numThreads={threads} &> {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}

diff --git a/rules/LepMap3/reorder.smk b/rules/LepMap3/reorder.smk
@@ -16,7 +16,7 @@ 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} &> {output.runlog}
+        zcat {input.datacall} | java -cp software/LepMap3 OrderMarkers2 evaluateOrder={input.lg_order} {params.extra} map={input.filt_map} data=- numThreads={threads} &> {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}