Add hiddendomains, pepr, zerone to the pipeline

chipathlon/conf.py

@@ -36,7 +36,10 @@ peak_tools = [
     "macs2",
     "gem",
     "peakranger",
-    "ccat"
+    "ccat",
+    "zerone",
+    "hiddendomains",
+    "pepr"
 ]
 
 # Peak_type validation
@@ -45,7 +48,10 @@ peak_types = {
     "macs2": ["narrow", "broad"],
     "gem": ["narrow"],
     "peakranger": ["narrow"],
-    "ccat": ["broad"]
+    "ccat": ["broad"],
+    "zerone": ["broad"],
+    "hiddendomains": ["broad"],
+    "pepr": ["narrow", "broad"]
 }
 
 # File extensions

chipathlon/generators/idr_generator.py

@@ -30,7 +30,10 @@ class IdrGenerator(ModuleGenerator):
             "ccat": ["region_sorted.bed", "peak_sorted.bed"],
             "gem": ["results_GEM_sorted.bed", "results_GPS_sorted.bed"],
             "spp": ["results_sorted.bed"],
-            "macs2": ["results_sorted.bed"]
+            "zerone": ["results_sorted_final.bed"],
+            "hiddendomains": ["results_final.bed"],
+            "macs2": ["results_sorted.bed"],
+            "pepr": ["pepr_result.bed"]
         }
         if debug:
             print "[LOADING GENERATOR] IdrGenerator"

chipathlon/generators/peak_call_generator.py

@@ -29,7 +29,10 @@ class PeakCallGenerator(ModuleGenerator):
             "spp": self._spp,
             "macs2": self._macs2,
             "ccat": self._ccat,
-            "peakranger": self._peakranger
+            "peakranger": self._peakranger,
+            "zerone": self._zerone,
+            "hiddendomains": self._hiddendomains,
+            "pepr": self._hiddendomains
         }
         self.call_pairs = {}
         if debug:
@@ -125,6 +128,53 @@ class PeakCallGenerator(ModuleGenerator):
         additional_inputs = {}
         return (self.get_markers(run), inputs, additional_inputs)
 
+    def _zerone(self, run, result):
+        """
+        :param run: The run to generate jobs for
+        :type run: :py:class:chipathlon.run.Run
+        :param result: The result to generate jobs for.
+        :type result: :py:class:chipathlon.result.Result
+        """
+        call_pair = self.call_pairs[result.full_name]
+        inputs = {
+            "control.bam": call_pair[0].full_name,
+            "exp.bam": call_pair[1].full_name
+        }
+        additional_inputs = {}
+        return (self.get_markers(run), inputs, additional_inputs)
+
+    def _hiddendomains(self, run, result):
+        """
+        :param run: The run to generate jobs for
+        :type run: :py:class:chipathlon.run.Run
+        :param result: The result to generate jobs for.
+        :type result: :py:class:chipathlon.result.Result
+        """
+        call_pair = self.call_pairs[result.full_name]
+        inputs = {
+            "chrom.sizes": run.genome.get_chrom_sizes()["name"],
+            "control.bed": call_pair[0].full_name,
+            "exp.bed": call_pair[1].full_name,
+            "prefix": result.prefix
+        }
+        additional_inputs = {}
+        return (self.get_markers(run), inputs, additional_inputs)
+
+    def _pepr(self, run, result):
+        """
+        :param run: The run to generate jobs for
+        :type run: :py:class:chipathlon.run.Run
+        :param result: The result to generate jobs for.
+        :type result: :py:class:chipathlon.result.Result
+        """
+        call_pair = self.call_pairs[result.full_name]
+        inputs = {
+            "control.bed": call_pair[0].full_name,
+            "signal.bed": call_pair[1].full_name
+        }
+        additional_inputs = {}
+        return (self.get_markers(run), inputs, additional_inputs)
+
     def _make_call_pairs(self, run, result_list):
         """
         :param run: The run currently being processed.
@@ -164,12 +214,23 @@ class PeakCallGenerator(ModuleGenerator):
         :param run: The target run to generate jobs for.
         :type run: :py:class:chipathlon.run.Run
         """
-        remove_duplicates_results = run.get_results("remove_duplicates", "no_dups_chr.bed")
+
+        if run.peak == "zerone":
+            print "zerone"
+            if run.file_type == "fastq":
+                results = run.get_results("align", "align.bam")
+            elif run.file_type == "bam":
+                results = run.get_results("download", "encode.bam")
+            # results = run.get_results("align", "align.bam")
+            print results
+        else:
+            results = run.get_results("remove_duplicates", "no_dups_chr.bed")
+       
         module_markers = {"peak_call": self.get_markers(run)}
 
         all_result_names = []
         final_results = self.module.get_all_final_results(self.get_markers(run))
-        for paired_result in self._make_call_pairs(run, remove_duplicates_results):
+        for paired_result in self._make_call_pairs(run, results):
             for i, final_result in enumerate(final_results):
                 final_result_name = final_result["file_name"]
                 if final_result_name not in all_result_names:
@@ -198,11 +259,23 @@ class PeakCallGenerator(ModuleGenerator):
         :param result: The target result to create jobs for.
         :type result: :py:class:chipathlon.result.Result
         """
-        remove_duplicate_results = run.get_results("remove_duplicates", "no_dups_chr.bed")
+
+        if run.peak == "zerone":
+            print "zerone"
+            if run.file_type == "fastq":
+                results = run.get_results("align", "align.bam")
+            elif run.file_type == "bam":
+                results = run.get_results("download", "encode.bam")
+            # results = run.get_results("align", "align.bam")
+            print results
+        else:
+            results = run.get_results("remove_duplicates", "no_dups_chr.bed")
+
+
         prev_results = []
         control_accessions = result.get_accessions("control")
         signal_accessions = result.get_accessions("signal")
-        for prev_result in remove_duplicate_results:
+        for prev_result in results:
             if (set(prev_result.get_accessions("control")).issubset(control_accessions) and
                 set(prev_result.get_accessions("signal")).issubset(signal_accessions)):
                 prev_results.append(prev_result)

chipathlon/jobs/modules/peak_call.yaml

@@ -245,3 +245,82 @@ peak_call:
             - results_sorted.bed:
                 type: file
                 final_result: true
+  - zerone[tool]:
+    - broad[peak_type]:
+      - zerone_callpeak:
+          inputs:
+            - control.bam:
+                type: file
+            - exp.bam:
+                type: file
+          additional_inputs: null
+          outputs:
+            - zerone_output.bed:
+                type: stdout
+      - sort_awk_sort_peaks:
+          inputs:
+            - zerone_output.bed:
+                type: file
+          additional_inputs: null
+          outputs:
+            - results_sorted.bed:
+                type: file
+      - zerone_add_columns:
+          inputs:
+            - results_sorted.bed:
+                type: file
+          additional_inputs: null
+          outputs:
+            - results_sorted_final.bed:
+                type: file
+                final_result: true
+  - hiddendomains[tool]:
+    - broad[peak_type]:
+      - hiddendomains_callpeak:
+          inputs:
+            - control.bed:
+                type: file
+            - exp.bed:
+                type: file  
+            - chrom.sizes:
+                type: file
+            - prefix:
+                type: string
+          additional_inputs: null
+          outputs:
+            - analysis.bed:
+                type: file
+            - vis.bed:
+                type: file
+            - domains.txt:
+                type: file
+            - control_bins.txt:
+                type: file
+            - treatment_bins.txt:
+                type: file
+      - hiddendomains_add_columns:
+          inputs:
+            - analysis.bed:
+                type: file
+          additional_inputs: null
+          outputs:
+            - results_final.bed:
+                type: file
+                final_result: true
+  - pepr[tool]:
+    - broad[peak_type]:
+      - pepr_callpeak:
+          inputs:
+            - control.bed:
+                type: file
+            - signal.bed:
+                type: file
+          additional_inputs: null
+          outputs:
+            - pepr_result.bed:
+                type: file
+                final_result: true
+            - pepr_parameters.txt:
+                type: file
+            - pepr_log.txt:
+                type: file

chipathlon/jobs/params/hiddendomains_add_columns.yaml

+hiddendomains_add_columns:
+  inputs:
+    - name: peak_result
+      type: file
+      file_type: bed
+  additional_inputs: null
+  outputs:
+    - name: full_result
+      type: file
+      file_type: bed
+  command: hiddendomains_add_columns.sh
+  arguments:
+    - "$inputs.0":
+        type: file
+        changeable: false
+        required: true
+        has_value: false
+    - "$outputs.0":
+        type: file
+        changeable: false
+        required: true
+        has_value: false
+  walltime: 2000
+  memory: 2000
+  cores: 1
+  nodes: 1

chipathlon/jobs/params/hiddendomains_callpeak.yaml

+hiddendomains_callpeak:
+  inputs:
+    - name: control_bed
+      type: file
+      file_type: bed
+    - name: signal_bed
+      type: file
+      file_type: bed
+    - name: chrom_sizes
+      type: file
+      file_type: chrom_sizes
+    - name: prefix
+      type: string
+  additional_inputs: null
+  outputs:
+    - name: hiddendomains_result
+      type: file
+      file_type: bed
+    - name: enriched_bins_vis
+      type: file
+      file_type: bed
+    - name: domains
+      type: file
+      file_type: txt
+    - name: control_bins
+      type: file
+      file_type: txt
+    - name: treatment_bins
+      type: file
+      file_type: txt
+  command: hiddendomains
+  arguments:
+    - "-B":
+        type: string 
+        changeable: false
+        required: true
+        has_value: false
+    - "-c":
+        type: file
+        changeable: false
+        required: true
+        has_value: true
+        default: "$inputs.0"
+    - "-t":
+        type: file
+        changeable: false
+        required: true
+        has_value: true
+        default: "$inputs.1"
+    - "-g":
+        type: file
+        changeable: false
+        required: true
+        has_value: true
+        default: "$inputs.2"
+    - "-o":
+        type: file
+        changeable: false
+        required: true
+        has_value: true
+        default: "$inputs.3"
+    - "-b":
+        type: numeric
+        changeable: true
+        required: true
+        has_value: true
+        default: 1000
+    - "-p":
+        type: numeric
+        changeable: true
+        required: true
+        has_value: true
+        default: 0
+    - "-q":
+        type: numeric
+        changeable: true
+        required: true
+        has_value: true
+        default: 30
+  walltime: 240
+  memory: 16000
+  cores: 1
+  nodes: 1

chipathlon/jobs/params/pepr_callpeak.yaml

+pepr_callpeak:
+  inputs:
+    - name: control
+      type: file
+      file_type: bed
+    - name: signal
+      type: file
+      file_type: bed
+  additional_inputs: null
+  outputs:
+    - name: pepr_result
+      type: file
+      file_type: bed
+    - name: pepr_parameters
+      type: file
+      file_type: txt
+    - name: pepr_log
+      type: file
+      file_type: txt
+  command: pepr
+  arguments:
+    - "-c":
+        type: file
+        changeable: false
+        required: true
+        has_value: true
+        default: "$inputs.0,$inputs.0"
+    - "-i":
+        type: file
+        changeable: false
+        required: true
+        has_value: true
+        default: "$inputs.1,$inputs.1"
+    - "-n":
+        type: string
+        changeable: true
+        required: false
+        has_value: true
+        default: "NA"
+    - "-f":
+        type: string
+        changeable: true
+        required: true
+        has_value: true
+        default: "bed"
+    - "-s":
+        type: numeric
+        changeable: true
+        required: false
+        has_value: true
+        default: 10
+    - "-w":
+        type: numeric
+        changeable: true
+        required: false
+        has_value: true
+        default: 100
+    - "--diff":
+        type: boolean
+        changeable: true
+        required: false
+        has_value: false
+    - "--threshold":
+        type: string
+        changeable: true
+        required: false
+        has_value: true
+        default: "1e-5"
+    - "--peaktype":
+        type: string
+        changeable: true
+        required: true
+        has_value: true
+        default: "broad"
+    - "--normalization":
+        type: string
+        changeable: true
+        required: false
+        has_value: true
+        default: "intra-group"
+    - "--keep-max-dup":
+        type: numeric
+        changeable: true
+        required: false
+        has_value: true
+        default: 10000000
+    - "--num-processors":
+        type: numeric
+        changeable: true
+        required: false
+        has_value: true
+        default: 1
+    - "--input-directory":
+        type: string
+        changeable: true
+        required: false
+        has_value: true
+        default: ""
+    - "--output-directory":
+        type: string
+        changeable: true
+        required: false
+        has_value: true
+        default: ""
+    - "--verbose":
+        type: string
+        changeable: false
+        required: true
+        has_value: false
+  walltime: 120
+  memory: 16000
+  cores: 1
+  nodes: 1

chipathlon/jobs/params/picard_mark_duplicates.yaml

@@ -8,8 +8,7 @@ picard_mark_duplicates:
     - name: dups_marked
       type: file
       file_type: bam
-
-    - name: quaality
+    - name: quality
       type: file
       file_type: qc
   command: picard

chipathlon/jobs/params/zerone_add_columns.yaml

+zerone_add_columns:
+  inputs:
+    - name: peak_result
+      type: file
+      file_type: bed
+  additional_inputs: null
+  outputs:
+    - name: full_result
+      type: file
+      file_type: bed
+  command: zerone_add_columns.sh
+  arguments:
+    - "$inputs.0":
+        type: file
+        changeable: false
+        required: true
+        has_value: false
+    - "$outputs.0":
+        type: file
+        changeable: false
+        required: true
+        has_value: false
+  walltime: 2000
+  memory: 2000
+  cores: 1
+  nodes: 1

chipathlon/jobs/params/zerone_callpeak.yaml

+zerone_callpeak:
+  inputs:
+    - name: control_bam
+      type: file
+      file_type: bam
+    - name: signal_bam
+      type: file
+      file_type: bam
+  additional_inputs: null
+  outputs:
+    - name: zerone_result
+      type: stdout
+      file_type: bed
+  command: zerone
+  arguments:
+    - "--mock":
+        type: file
+        changeable: false
+        required: true
+        has_value: true
+        default: "$inputs.0"
+    - "--chip":
+        type: file
+        changeable: false
+        required: true
+        has_value: true
+        default: "$inputs.1"
+    - "--window":
+        type: numeric
+        changeable: true
+        required: true
+        has_value: true
+        default: 300
+    - "--quality":
+        type: numeric
+        changeable: true
+        required: true
+        has_value: true
+        default: 20
+  walltime: 120
+  memory: 16000
+  cores: 1
+  nodes: 1

chipathlon/jobs/scripts/hiddendomains_add_columns.sh

+#!/bin/bash
+
+awk '{print $0,0,0,0,0,0}' "$1" > "$2"

chipathlon/jobs/scripts/zerone_add_columns.sh

+#!/bin/bash
+
+awk '{print $0,0,0}' "$1" > "$2"

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