update tests

.travis.yml

@@ -109,6 +109,7 @@ install:
   - conda update -q conda
   # Useful for debugging any issues with conda
   - conda info -a
+  - conda activate base
   - conda install -c bioconda transdecoder 
   - conda install -c bioconda diamond
 

pyrpipe/sra.py

@@ -419,11 +419,14 @@ def run_fasterqdump(self,delete_sra=False,verbose=False,quiet=False,logs=True,**
             del kwargs['-o']
 
 
+        #determine threads if not specified
+        if '-e' not in kwargs:
+            kwargs['-e']=str(self.threads)
         #execute command
 
         fstrqd_Cmd=['fasterq-dump']
         fstrqd_Cmd.extend(pu.parse_unix_args(fasterqdumpArgsList,kwargs))
-        fstrqd_Cmd.extend(['-e',str(self.threads)])
+
         #add location
         fstrqd_Cmd.extend(['-O',self.location])
         #add output filename. output will be <srr_accession>.fastq or <srr_accession>_1.fastq and <srr_accession>_2.fastq

tests/test_integration.py

@@ -28,7 +28,7 @@ def test_pipeline1():
     st=sraOb.download_sra()
     assert st==True,"SRA download failed"
 
-    st=sraOb.run_fasterqdump(delete_sra=False,**{"-e":"8","-f":"","-t":workingDir})
+    st=sraOb.run_fasterqdump(delete_sra=False,**{"-f":"","-t":workingDir})
     assert st==True,"fqdump failed"
 
     bbdOpts={"ktrim":"r","k":"23","mink":"11","qtrim":"'rl'","trimq":"10","--":("-Xmx2g",),"ref":testVars.bbdukAdapters}