Fixed lots of minor bugs to make sure the workflow actually generates! Running tests now.

chipathlon/conf.py

@@ -69,8 +69,8 @@ executables = [
     "chip-job-peakranger-format",
     "chip-job-sort-peak",
     "chip-job-zcat-peak",
-    "chip-job-zerone-add-cols",
-    "chip-job-hd-add-cols"
+    "chip-job-zerone-format",
+    "chip-job-hd-format"
 ]
 
 # Java needs to have -Xmx specified...

chipathlon/generators/peak_call_generator.py

@@ -161,8 +161,7 @@ class PeakCallGenerator(ModuleGenerator):
             "control.bam": call_pair[0].full_name,
             "signal.bam": call_pair[1].full_name
         }
-        additional_inputs = {}
-        return (self.get_markers(run), inputs, additional_inputs)
+        return (self.get_markers(run), inputs)
 
     def _hiddendomains(self, run, result):
         """
@@ -178,8 +177,7 @@ class PeakCallGenerator(ModuleGenerator):
             "signal.bed": call_pair[1].full_name,
             "prefix": result.prefix
         }
-        additional_inputs = {}
-        return (self.get_markers(run), inputs, additional_inputs)
+        return (self.get_markers(run), inputs) 
 
     def _pepr(self, run, result):
         """
@@ -195,8 +193,7 @@ class PeakCallGenerator(ModuleGenerator):
             "prefix": result.prefix,
             "peak_type": run.peak_type
         }
-        additional_inputs = {}
-        return (self.get_markers(run), inputs, additional_inputs)
+        return (self.get_markers(run), inputs) 
 
     def _make_call_pairs(self, run, result_list):
         """

chipathlon/jobs/modules/peak_call.yaml

@@ -337,7 +337,7 @@ peak_call:
             chrom.sizes:
               param_name: chrom_sizes
             prefix:
-              type: string
+              param_name: prefix
           outputs:
             result.bed:
               param_name: result_peaks
@@ -352,10 +352,10 @@ peak_call:
       - hiddendomains_format:
           inputs:
             result.bed:
-              type: file
+              param_name: result_peaks
           outputs:
             results_sorted.bed:
-              type: file
+              param_name: full_result
               final_result: true
   - pepr[tool]:
     - pepr_callpeak:

chipathlon/jobs/params/hiddendomains_callpeak.yaml

@@ -23,11 +23,11 @@ hiddendomains_callpeak:
       file_type: txt
     control_bins:
       type: file
-      file_type: bxt
+      file_type: txt
     treatment_bins:
       type: file
       file_type: txt
-  command: hiddendomains
+  command: hiddenDomains
   arguments:
     - "-B":
         type: string
@@ -53,7 +53,7 @@ hiddendomains_callpeak:
         has_value: true
         default: "$chrom_sizes"
     - "-o":
-        type: file
+        type: string
         changeable: false
         required: true
         has_value: true

chipathlon/jobs/params/hiddendomains_format.yaml

@@ -3,7 +3,6 @@ hiddendomains_format:
     result_peaks:
       type: file
       file_type: bed
-  additional_inputs: null
   outputs:
     full_result:
       type: file

chipathlon/jobs/params/pepr_callpeak.yaml

@@ -17,7 +17,7 @@ pepr_callpeak:
     pepr_params:
       type: file
       file_type: txt
-  command: pepr
+  command: PePr
   arguments:
     - "-c":
         type: list
@@ -38,7 +38,7 @@ pepr_callpeak:
           - $signal.bed
           - $signal.bed
     - "-n":
-        type: file
+        type: string
         changeable: true
         required: true
         has_value: true

chipathlon/jobs/wrappers/hiddendomains_wrapper.sh

-#!/bin/bash
-
-. /util/opt/lmod/lmod/init/profile
-module load hiddendomains/2.3
-
-hiddenDomains "$@"

chipathlon/jobs/wrappers/pepr_wrapper.sh

-#!/bin/bash
-
-. /util/opt/lmod/lmod/init/profile
-module load pepr/1.1
-
-PePr "$@"

chipathlon/jobs/wrappers/picard_wrapper.sh

-#!/bin/bash
-#set -eu -o pipefail
-#set -o pipefail
-
-. /util/opt/lmod/lmod/init/profile
-module load picard/2.9
-
-# Use Java installed with Anaconda to ensure correct version
-java="$ENV_PREFIX/bin/java"
-
-# if JAVA_HOME is set (non-empty), use it. Otherwise keep "java"
-if [ ! -z "${JAVA_HOME:=}" ]; then
-  if [ -e "$JAVA_HOME/bin/java" ]; then
-      java="$JAVA_HOME/bin/java"
-  fi
-fi
-
-picard "$@"
-

chipathlon/jobs/wrappers/zerone_wrapper.sh

-#!/bin/bash
-
-. /util/opt/lmod/lmod/init/profile
-module load zerone/1.0
-
-zerone "$@"

chipathlon/workflow.py

@@ -242,7 +242,6 @@ class Workflow(object):
         # Load each yaml_job as an actual object
         for root, dirs, files in os.walk("%s/%s" % (os.path.dirname(os.path.realpath(__file__)), chipathlon.conf.job_params)):
             for f in files:
-                print(f)
                 yaml_job = chipathlon.workflow_job.WorkflowJob(os.path.join(root, f), self.params.get(f.split(".")[0]), self.debug)
                 if yaml_job.is_valid():
                     if yaml_job.command in self.executables:

chipathlon/workflow_job.py

@@ -566,9 +566,9 @@ class WorkflowJob(object):
             # Need to figure out 2 things:
             # 1. Should we add the argument name?
             # 2. What's the correct value to add?
-            add_value = self._interpolate_value(inputs, outputs, arg_name, arg_info)
             if self.debug:
-                print "%s: Loading argument: %s, info: %s, value: %s" % (self, arg_name, arg_info, add_value)
+                print "\t%s: Loading argument: %s, info: %s" % (self, arg_name, arg_info)
+            add_value = self._interpolate_value(inputs, outputs, arg_name, arg_info)
             # Only add arguments that have a value
             if add_value is not None:
                 # Need to add in the arg_name and the arg_value

setup.py

@@ -22,7 +22,9 @@ setup(
         "scripts/chip-job-peakranger-format",
         "scripts/chip-job-save-result",
         "scripts/chip-job-sort-peak",
-        "scripts/chip-job-zcat-peak"
+        "scripts/chip-job-zcat-peak",
+        "scripts/chip-job-zerone-format",
+        "scripts/chip-job-hd-format"
     ],
     install_requires=["pymongo","pyyaml"],
     zip_safe=False