diff qualimap_bamqc.py @ 30:418ee04dd1b2 draft

planemo upload for repository https://github.com/scottx611x/qualimap2 commit dc78b7c4b1780b316ca4aba2be247969ac1100ec-dirty

--- a/qualimap_bamqc.py	Thu Jul 26 16:21:44 2018 -0400
+++ b/qualimap_bamqc.py	Thu Jul 26 16:40:19 2018 -0400
@@ -2,17 +2,18 @@
 from __future__ import print_function
 import argparse
 from subprocess import check_call, CalledProcessError
-import os
 import shutil
 import sys
 
+OUTPUT_DIR = "qualimap_results"
+
 
 def qualimap_bamqc(bam_filename, genomecov_file, jv_mem_size):
     qualimap_command = [
         "qualimap", "bamqc",
         "-bam " + bam_filename,
         "-oc " + genomecov_file,
-        "-outdir .",
+        "-outdir " + OUTPUT_DIR,
         "--java-mem-size=" + jv_mem_size
     ]
 
@@ -38,12 +39,12 @@
         args.java_mem_size
     )
 
-    print(os.listdir("../"))
-
+    shutil.move(OUTPUT_DIR + "/genome_results.txt", "genome_results.txt")
+    shutil.move(OUTPUT_DIR + "/qualimapReport.html", "qualimapReport.html")
     shutil.make_archive(
         'raw_data_qualimapReport',
         'zip',
-        os.path.join("../", 'raw_data_qualimapReport')
+        OUTPUT_DIR + '/raw_data_qualimapReport'
     )