fix download ftp links

ktmeaton · Sep 7, 2021 · b4729f1 · b4729f1
1 parent 6538c5c
commit b4729f1
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Showing 2 changed files with 5 additions and 3 deletions.
diff --git a/workflow/rules/download.smk b/workflow/rules/download.smk
@@ -38,7 +38,7 @@ rule download_assembly:
 	      reads_origin = "(reference|assembly)",
     params:
 		    ftp = lambda wildcards: [
-          ftp for ftp in
+          "{}.{}.gz".format(ftp, wildcards.ext) for ftp in
           globals()["identify_" + wildcards.reads_origin + "_ftp"]()
           if wildcards.sample in ftp][0]
     resources:

diff --git a/workflow/rules/functions.smk b/workflow/rules/functions.smk
@@ -27,7 +27,8 @@ def identify_reference_ftp():
     conn = sqlite3.connect(sqlite_db_path)
     cur = conn.cursor()
     ref_url = cur.execute(config["sqlite_select_command_ref"]).fetchone()[0]
-    ref_fna_gz = ref_url.split("/")[9] + "_genomic.fna.gz"
+    #ref_fna_gz = ref_url.split("/")[9] + "_genomic.fna.gz"
+    ref_fna_gz = ref_url.split("/")[9] + "_genomic"
     ref_url = [ref_url + "/" + ref_fna_gz]
     cur.close()
     return ref_url
@@ -66,7 +67,8 @@ def identify_assembly_ftp():
             if len(asm_ftp_list) >= max_datasets:
                 break
             if url:
-                asm_ftp_list.append(url + "/"+ url.split("/")[9] + "_genomic.fna.gz")
+                #asm_ftp_list.append(url + "/"+ url.split("/")[9] + "_genomic.fna.gz")
+                asm_ftp_list.append(url + "/"+ url.split("/")[9] + "_genomic")
     cur.close()
     return asm_ftp_list