deleting some files

Author: conchoecia

meta_scripts/GAP_hicanu_pt1

@@ -40,3 +40,4 @@ rule assemble:
           genomeSize={params.genome_size} \
           -pacbio-hifi {params.LR_string}
         """
+

meta_scripts/GAP_hifiasm_pt1

@@ -12,11 +12,15 @@ for x in check_these:
     if x not in config:
         raise IOError("The option '{}' must be in the config".format(x))
 
+if "hifiasm_options" not in config:
+    config["hifiasm_options"] = ""
+
 rule all:
     # genome assem
     input:
-        "step1_hifiasm_hic/" + config["prefix"] + ".hic.hap1.p_ctg.gfa",
-        "step1_hifiasm_hic/" + config["prefix"] + ".hic.hap2.p_ctg.gfa"
+        expand("step1_hifiasm_hic/" + config["prefix"] + ".hic.hap{hap}.p_ctg.fasta",
+               hap = ["1", "2"])
+
 
 rule assemble:
     input:
@@ -31,6 +35,7 @@ rule assemble:
         hic_R1_string = ",".join([config["HiC"][lib]["R1"] for lib in config["HiC"]]),
         hic_R2_string = ",".join([config["HiC"][lib]["R2"] for lib in config["HiC"]]),
         LR_string     = " ".join(config["LR"]),
+        hifiasm_opts  = config["hifiasm_options"],
         prefix        = config["prefix"]
     shell:
         """
@@ -41,6 +46,20 @@ rule assemble:
           --h1 {params.hic_R1_string} \
           --h2 {params.hic_R2_string} \
           --n-weight 5 \
-           {params.LR_string}
+          {params.hifiasm_opts} \
+          {params.LR_string}
         cd ..
         """
+
+rule gfa_to_fasta:
+    input:
+        gfa = "step1_hifiasm_hic/" + config["prefix"] + ".hic.hap{hap}.p_ctg.gfa",
+    output:
+        gfa = "step1_hifiasm_hic/" + config["prefix"] + ".hic.hap{hap}.p_ctg.fasta",
+    threads: 1
+    shell:
+        """
+        cat {input.gfa} | \
+          awk '{{if ($1 == "S"){{printf(">%s\\n%s\\n", $2, $3)}} }}' | \
+          fold -60 > {output.gfa}
+        """