Merge pull request #42 from xin-huang/codex/reorder-outlier-gene-rules

Extract gene column before filtering semicolons to avoid dropping genes in outlier lists

Author: nomis-c

workflow/rules/4.1_positive_selection_selscan.smk

@@ -178,7 +178,7 @@ rule get_selscan_outlier_genes:
         "../envs/selscape-env.yaml"
     shell:
         """
-        ( sed '1d' {input.selscan_outliers} | grep -v ";" | awk '{{print $7}}' | sort | uniq > {output.selscan_genes} ) 2> {log} || true
+        ( sed '1d' {input.selscan_outliers} | awk '{{print $7}}' | grep -v ";" | sort | uniq > {output.selscan_genes} ) 2> {log} || true
         sed -i '1iGene' {output.selscan_genes} 2>> {log}
         """
 

workflow/rules/4.2_positive_selection_selscan_xp.smk

@@ -201,7 +201,7 @@ rule get_selscan_xp_outlier_genes:
         "../envs/selscape-env.yaml"
     shell:
         """
-        ( sed '1d' {input.selscan_xp_outliers} | grep -v ";" | awk '{{print $7}}' | sort | uniq > {output.selscan_xp_genes} ) 2> {log} || true
+        ( sed '1d' {input.selscan_xp_outliers} | awk '{{print $7}}' | grep -v ";" | sort | uniq > {output.selscan_xp_genes} ) 2> {log} || true
         sed -i '1iGene' {output.selscan_xp_genes} 2>> {log}
         """
 

workflow/rules/4.3_positive_selection_scikit-allel.smk

@@ -175,7 +175,7 @@ rule get_tajima_d_outlier_genes:
         "../envs/selscape-env.yaml"
     shell:
         """
-        ( sed '1d' {input.tajima_d_outliers} | grep -v ";" | awk '{{print $7}}' | sort | uniq > {output.tajima_d_genes} ) 2> {log} || true
+        ( sed '1d' {input.tajima_d_outliers} | awk '{{print $7}}' | grep -v ";" | sort | uniq > {output.tajima_d_genes} ) 2> {log} || true
         sed -i '1iGene' {output.tajima_d_genes} 2>> {log}
         """
 

workflow/rules/4.4_positive_selection_scikit-allel_xp.smk

@@ -174,7 +174,7 @@ rule get_delta_tajima_d_outlier_genes:
         "../envs/selscape-env.yaml"
     shell:
         """
-        ( sed '1d' {input.delta_outliers} | grep -v ";" | awk '{{print $7}}' | sort | uniq > {output.delta_genes} ) 2> {log} || true
+        ( sed '1d' {input.delta_outliers} | awk '{{print $7}}' | grep -v ";" | sort | uniq > {output.delta_genes} ) 2> {log} || true
         sed -i '1iGene' {output.delta_genes} 2>> {log}
         """
 

workflow/rules/5.1_balancing_selection_betascan.smk

@@ -143,7 +143,7 @@ rule get_betascan_outlier_genes:
         "../envs/selscape-env.yaml"
     shell:
         """
-        ( sed '1d' {input.betascan_outliers} | grep -v ";" | awk '{{print $7}}' | sort | uniq > {output.betascan_genes} ) 2> {log} || true
+        ( sed '1d' {input.betascan_outliers} | awk '{{print $7}}' | grep -v ";" | sort | uniq > {output.betascan_genes} ) 2> {log} || true
         sed -i '1iGene' {output.betascan_genes} 2>> {log}
         """
 

workflow/rules/5.2_balancing_selection_scikit-allel.smk

@@ -173,7 +173,7 @@ rule get_tajima_d_balancing_outlier_genes:
         "../envs/selscape-env.yaml"
     shell:
         """
-        ( sed '1d' {input.tajima_d_outliers} | grep -v ";" | awk '{{print $7}}' | sort | uniq > {output.tajima_d_genes} ) 2> {log} || true
+        ( sed '1d' {input.tajima_d_outliers} | awk '{{print $7}}' | grep -v ";" | sort | uniq > {output.tajima_d_genes} ) 2> {log} || true
         sed -i '1iGene' {output.tajima_d_genes} 2>> {log}
         """