update travis

.travis.yml

@@ -109,14 +109,8 @@ install:
   - conda update -q conda
   # Useful for debugging any issues with conda
   - conda info -a
-  - cd tests
-  - bash build_test_env.sh
-  - conda activate pyrpipe_test
-  - cd ..
   - conda install -c bioconda transdecoder 
   - conda install -c bioconda diamond
-  #use docker portculllis
-  - export PATH=$PATH:$PWD/portcullisDocker/
 
 
 

pyrpipe/mapping.py

@@ -423,7 +423,7 @@ def build_index(self,index_path,*args,verbose=False,quiet=False,logs=True,object
 
 
 
-    def perform_alignment(self,sra_object,out_suffix="_star",out_dir="",verbose=False,quiet=False,logs=True,objectid="NA",out_type=None,optimize=None,**kwargs):
+    def perform_alignment(self,sra_object,out_suffix="_star",out_dir="",verbose=False,quiet=False,logs=True,objectid="NA",out_type=None,optimize=None,threads=None,**kwargs):
         """Function to perform alignment using star and the provided SRA object.
         All star output will be written to the sra_object directory by default.
         
@@ -445,9 +445,11 @@ def perform_alignment(self,sra_object,out_suffix="_star",out_dir="",verbose=Fals
         objectid: str
             Provide an id to attach with this command e.g. the SRR accession. This is useful for debugging, benchmarking and reports.
         out_type: str
-            Out type options for star
+            Out type options for star: sam, sorted_bam, unsorted_bam [Default: sorted_bam]
         optimize: bool
-            If true optimize maping parameters based on read length
+            If true optimize maping parameters based on read length [Default: True]
+        threads: int
+            Num threads to use. If supplied will override threads supplied during __init__
         kwargs: dict
             Options to pass to STAR. This will override the existing options in self.passed_args_dict (only replace existing arguments and not replace all the arguments).
         
@@ -456,6 +458,7 @@ def perform_alignment(self,sra_object,out_suffix="_star",out_dir="",verbose=Fals
         :rtype: string
         """
 
+
         if not out_dir:
             out_dir=sra_object.location
         else:
@@ -472,6 +475,10 @@ def perform_alignment(self,sra_object,out_suffix="_star",out_dir="",verbose=Fals
         #add out dir
         newOpts["--outFileNamePrefix"]=out_dir+"/"
 
+        #determine threads
+        #use
+
+
 
         #add input files to kwargs, overwrite kwargs with newOpts
         mergedOpts={**kwargs,**newOpts}