stacks 2.2 step4 update

00-scripts/step4.sf

@@ -51,12 +51,13 @@ rule run_populations:
     params:
         r=config["populations"]["r"],
         p=config["populations"]["p"],
-        f=config["populations"]["f"],
-        a=config["populations"]["a"],
+        fst_correction=config["populations"]["fst_correction"],
+        min_maf=config["populations"]["min_maf"],
         p_value_cutoff=config["populations"]["p_value_cutoff"],
-        lnl_lim=config["populations"]["lnl_lim"]
+        lnl_lim=config["populations"]["lnl_lim"],
+        renz=config["populations"]["renz"]
     log:
         '10-logs/populations/{species}.log'
     shell:
         '''mkdir -p {output};
-        populations -t {threads} -P {input.gdir} -M {input.popm} -r {params.r} -p {params.p} -f {params.f} -a {params.a} --p_value_cutoff {params.p_value_cutoff} --lnl_lim {params.lnl_lim} --write_single_snp --vcf --vcf_haplotypes --structure -O {output} > {log}'''
+        populations -t {threads} -P {input.gdir} -M {input.popm} -r {params.r} --fst_correction {params.fst_correction} --min_maf {params.min_maf} --p_value_cutoff {params.p_value_cutoff} --lnl_lim {params.lnl_lim} --write_single_snp --vcf --vcf_haplotypes --merge_sites --renz {params.renz} --structure -O {output} > {log}'''

01-info_files/config.yaml

@@ -21,9 +21,11 @@ gstacks:
 populations:
     cores : 32
     r : 0.85
-    p : 1
-    f : p_value
-    a : 0.05
+    p : 4
+    fst_correction : p_value
+    min_maf : 0.05
     p_value_cutoff : 0.10
     lnl_lim : -10
+    renz : SbfI
+