Merge pull request #24 from icgc-argo/prep-sanger-supplement.0.1.2.0

Prep sanger supplement.0.1.2.0

tools/prep-sanger-supplement/prep-sanger-supplement.nf

@@ -23,7 +23,7 @@
  */
 
 nextflow.preview.dsl = 2
-version = '0.1.1.0'
+version = '0.1.2.0'
 
 params.result_tars = ""
 params.container_version = ""

tools/prep-sanger-supplement/prep-sanger-supplement.py

@@ -50,21 +50,21 @@ def main(args):
 
         # untar and remove unneeded files
         if tool_name == 'timings':
-            cmd = "tar -xf %s -C %s && rm -fr %s/*.brm.bam %s/*.brm.bam.bai %s/*.intermediates.tar.gz %s/*.bw" % \
-                (tar, '.', tool_name, tool_name, tool_name, tool_name)
+            cmd = 'tar -xf %s -C %s && ' % (tar, '.')
         else:
-            cmd = "mkdir %s && tar -xf %s -C %s && rm -fr %s/*.intermediates.tar.gz %s/*.bw" % \
-                (tool_name, tar, tool_name, tool_name, tool_name)
+            cmd = 'mkdir %s && tar -xf %s -C %s && ' % (tool_name, tar, tool_name)
 
+        cmd = cmd + "rm -fr %s/*.brm.bam %s/*.brm.bam.bai %s/*.intermediates.tar.gz %s/*.bw" % \
+                        tuple([tool_name] * 4)
         run_cmd(cmd)
 
         extra_info = {
             "description": description[tool_name],
-            "files": []
+            "files_in_tgz": []
         }
 
         for f in sorted(glob.glob(f"{tool_name}/*")):
-            extra_info['files'].append(f.split(os.sep)[1])
+            extra_info['files_in_tgz'].append(f.split(os.sep)[1])
 
 
         extra_info_file = 'sanger.%s-supplement.extra_info.json' % tool_name

tools/prep-sanger-supplement/tests/test-2.nf.json

@@ -0,0 +1,9 @@
+{
+  "result_tars": [
+    "input/WXS_SA610229_vs_SA610228.timings.tar.gz",
+    "input/WXS_SA610229_vs_SA610228.caveman.tgz",
+    "input/WXS_SA610229_vs_SA610228.pindel.tgz",
+    "input/WXS_SA610229_vs_SA610228.ascat.tgz",
+    "input/WXS_SA610229_vs_SA610228.brass.tgz"
+  ]
+}