Updates to make sure jobs get loaded correctly with executable changes.

chipathlon/conf.py

@@ -45,8 +45,15 @@ executables = [
     "bamtools",
     "samtools",
     "idr",
-    "picard"
-] + align_tools + peak_tools
+    "picard",
+    "bwa",
+    "bowtie2",
+    "macs2",
+    "gem",
+    "peakranger",
+    "MUSIC",
+    "CCAT"    
+]
 
 # Peak_type validation
 peak_types = {

chipathlon/jobs/params/ccat_callpeak.yaml

@@ -35,7 +35,7 @@ ccat_callpeak:
     - name: ccat_log
       type: stdout
       file_type: log
-  command: ccat
+  command: CCAT
   arguments:
     - "$inputs.0":
         type: file

chipathlon/jobs/params/music_broad.yaml

@@ -42,7 +42,7 @@ music_broad:
     - name: scale_16626.bed
       type: file
       file_type: bed
-  command: music
+  command: MUSIC
   arguments:
     - "--prefix":
         type: string

chipathlon/jobs/params/music_narrow.yaml

@@ -26,7 +26,7 @@ music_narrow:
     - name: scale_291.bed
       type: file
       file_type: bed
-  command: music
+  command: MUSIC
   arguments:
     - "--prefix":
         type: string

chipathlon/jobs/params/music_punctate.yaml

@@ -46,7 +46,7 @@ music_punctate:
     - name: scale_2216.bed
       type: file
       file_type: bed
-  command: music
+  command: MUSIC
   arguments:
     - "--prefix":
         type: string

chipathlon/jobs/params/spp_nodups_broad.yaml

@@ -20,7 +20,7 @@ spp_nodups_broad:
     - name: score
       type: file
       file_type: ccscore
-  command: spp_nodups
+  command: run_spp_nodups
   arguments:
     - "-c=":
         type: file

chipathlon/jobs/params/spp_nodups_narrow.yaml

@@ -20,7 +20,7 @@ spp_nodups_narrow:
     - name: score
       type: file
       file_type: ccscore
-  command: spp_nodups
+  command: run_spp_nodups
   arguments:
     - "-c=":
         type: file

chipathlon/workflow_job.py

@@ -481,6 +481,8 @@ class WorkflowJob(object):
             "$outputs": outputs
         }
         arg_list = []
+        if self.executable == "gem":
+            arg_list.append("-Xmx%sM" % (self.params.get("memory", self.job_data["memory"])))
         has_args = re.compile("\$((in)|(out))puts\.[0-9]")
         # Loop through each argument, which are stored as a list of dicts
         for arg_dict in self.job_data["arguments"]: