diff --git a/.travis.yml b/.travis.yml#
similarity index 100%
rename from .travis.yml
rename to .travis.yml#
diff --git a/cwl_awsem/repliseq/align_pe.cwl b/cwl_awsem/repliseq/align_pe.cwl
new file mode 100644
index 0000000..8b0b452
--- /dev/null
+++ b/cwl_awsem/repliseq/align_pe.cwl
@@ -0,0 +1,98 @@
+{
+    "hints": [
+        {
+            "dockerPull": "duplexa/4dn-repliseq:v9",
+            "class": "DockerRequirement"
+        }
+    ],
+    "arguments": [],
+    "class": "CommandLineTool",
+    "inputs": [
+        {
+            "type": [
+                "File"
+            ],
+            "id": "#fastq1",
+            "inputBinding": {
+                "position": 1,
+                "separate": true
+            }
+        },
+        {
+            "type": [
+                "File"
+            ],
+            "id": "#fastq2",
+            "inputBinding": {
+                "position": 2,
+                "separate": true
+            }
+        },
+        {
+            "type": [
+                "File"
+            ],
+            "id": "#bwa_index",
+            "inputBinding": {
+                "position": 3,
+                "separate": true
+            }
+        },
+        {
+            "type": [
+                "int"
+            ],
+            "id": "#nThreads",
+            "inputBinding": {
+                "position": 6,
+                "separate": true
+            },
+            "default": 4
+        },
+        {
+            "type": [
+                "null",
+                "string"
+            ],
+            "id": "#prefix",
+            "inputBinding": {
+                "position": 5,
+                "separate": true
+            },
+            "default": "out"
+        },
+        {
+            "type": [
+                "null",
+                "string"
+            ],
+            "id": "#outdir",
+            "inputBinding": {
+                "position": 4,
+                "separate": true
+            },
+            "default": "."
+        }
+    ],
+    "outputs": [
+        {
+            "type": [
+                "null",
+                "File"
+            ],
+            "id": "#out_bam",
+            "outputBinding": {
+                "glob": "*.bam"
+            }
+        }
+    ],
+    "baseCommand": [
+        "run-align-pe.sh"
+    ],
+    "requirements": [
+        {
+            "class": "InlineJavascriptRequirement"
+        }
+    ],
+    "cwlVersion": "draft-3"
+}
diff --git a/cwl_awsem/repliseq/align_se.cwl b/cwl_awsem/repliseq/align_se.cwl
new file mode 100644
index 0000000..aec901b
--- /dev/null
+++ b/cwl_awsem/repliseq/align_se.cwl
@@ -0,0 +1,88 @@
+{
+    "hints": [
+        {
+            "dockerPull": "duplexa/4dn-repliseq:v9",
+            "class": "DockerRequirement"
+        }
+    ],
+    "arguments": [],
+    "class": "CommandLineTool",
+    "inputs": [
+        {
+            "type": [
+                "File"
+            ],
+            "id": "#fastq1",
+            "inputBinding": {
+                "position": 1,
+                "separate": true
+            }
+        },
+        {
+            "type": [
+                "File"
+            ],
+            "id": "#bwa_index",
+            "inputBinding": {
+                "position": 2,
+                "separate": true
+            }
+        },
+        {
+            "type": [
+                "int"
+            ],
+            "id": "#nThreads",
+            "inputBinding": {
+                "position": 5,
+                "separate": true
+            },
+            "default": 4
+        },
+        {
+            "type": [
+                "null",
+                "string"
+            ],
+            "id": "#prefix",
+            "inputBinding": {
+                "position": 4,
+                "separate": true
+            },
+            "default": "out"
+        },
+        {
+            "type": [
+                "null",
+                "string"
+            ],
+            "id": "#outdir",
+            "inputBinding": {
+                "position": 3,
+                "separate": true
+            },
+            "default": "."
+        }
+    ],
+    "outputs": [
+        {
+            "type": [
+                "null",
+                "File"
+            ],
+            "id": "#out_bam",
+            "outputBinding": {
+                "glob": "*.bam"
+            }
+        }
+    ],
+    "baseCommand": [
+        "run-align-se.sh"
+    ],
+    "requirements": [
+        {
+            "class": "InlineJavascriptRequirement"
+        }
+    ],
+    "cwlVersion": "draft-3"
+}
diff --git a/cwl_awsem/repliseq/clip.cwl b/cwl_awsem/repliseq/clip.cwl
new file mode 100644
index 0000000..67e5053
--- /dev/null
+++ b/cwl_awsem/repliseq/clip.cwl
@@ -0,0 +1,77 @@
+{
+    "hints": [
+        {
+            "dockerPull": "duplexa/4dn-repliseq:v9",
+            "class": "DockerRequirement"
+        }
+    ],
+    "arguments": [],
+    "class": "CommandLineTool",
+    "inputs": [
+        {
+            "type": [
+                "File"
+            ],
+            "id": "#input_fastq",
+            "inputBinding": {
+                "position": 1,
+                "separate": true
+            }
+        },
+        {
+            "type": [
+                "null",
+                "string"
+            ],
+            "id": "#outprefix",
+            "inputBinding": {
+                "position": 2,
+                "separate": true
+            },
+            "default": "out"
+        },
+        {
+            "type": [
+                "null",
+                "string"
+            ],
+            "id": "#outdir",
+            "inputBinding": {
+                "position": 1,
+                "separate": true
+            },
+            "default": "."
+        }
+    ],
+    "outputs": [
+        {
+            "type": [
+                "null",
+                "File"
+            ],
+            "id": "#out_clipped_fastq",
+            "outputBinding": {
+                "glob": "$(inputs.outdir + '/' + inputs.outprefix + '.clip.fastq')"
+            }
+        },
+        {
+            "type": [
+                "null",
+                "File"
+            ],
+            "id": "#out_log",
+            "outputBinding": {
+                "glob": "$(inputs.outdir + '/' + inputs.outprefix + '.clip.fastq.log')"
+            }
+        }
+    ],
+    "baseCommand": [
+        "clip"
+    ],
+    "requirements": [
+        {
+            "class": "InlineJavascriptRequirement"
+        }
+    ],
+    "cwlVersion": "draft-3"
+}
diff --git a/cwl_awsem/repliseq/count.cwl b/cwl_awsem/repliseq/count.cwl
new file mode 100644
index 0000000..ac7cdf7
--- /dev/null
+++ b/cwl_awsem/repliseq/count.cwl
@@ -0,0 +1,100 @@
+{
+    "hints": [
+        {
+            "dockerPull": "duplexa/4dn-repliseq:v9",
+            "class": "DockerRequirement"
+        }
+    ],
+    "arguments": [],
+    "class": "CommandLineTool",
+    "inputs": [
+        {
+            "type": [
+                "File"
+            ],
+            "id": "#input_bam",
+            "inputBinding": {
+                "position": 1,
+                "separate": true
+            }
+        },
+        {
+            "type": [
+                "null",
+                "File"
+            ],
+            "inputBinding": {
+                "separate": true,
+                "position": 2
+            },
+            "id": "#chrsizes"
+        },
+        {
+            "type": [
+                "int"
+            ],
+            "id": "#winsize",
+            "inputBinding": {
+                "position": 5,
+                "separate": true
+            },
+            "default": 5000
+        },
+        {
+            "type": [
+                "int"
+            ],
+            "id": "#minsize",
+            "inputBinding": {
+                "position": 6,
+                "separate": true
+            },
+            "default": 10000000
+        },
+        {
+            "type": [
+                "null",
+                "string"
+            ],
+            "id": "#outprefix",
+            "inputBinding": {
+                "position": 4,
+                "separate": true
+            },
+            "default": "out"
+        },
+        {
+            "type": [
+                "null",
+                "string"
+            ],
+            "id": "#outdir",
+            "inputBinding": {
+                "position": 3,
+                "separate": true
+            },
+            "default": "."
+        }
+    ],
+    "outputs": [
+        {
+            "type": [
+                "null",
+                "File"
+            ],
+            "id": "#out_count_bg",
+            "outputBinding": {
+                "glob": "$(inputs.outdir + '/' + inputs.outprefix + '.w' + inputs.winsize + '.bg')"
+            }
+        }
+    ],
+    "baseCommand": [
+        "count"
+    ],
+    "requirements": [
+        {
+            "class": "InlineJavascriptRequirement"
+        }
+    ],
+    "cwlVersion": "draft-3"
+}
diff --git a/cwl_awsem/repliseq/dedup.cwl b/cwl_awsem/repliseq/dedup.cwl
new file mode 100644
index 0000000..8f9fb85
--- /dev/null
+++ b/cwl_awsem/repliseq/dedup.cwl
@@ -0,0 +1,77 @@
+{
+    "hints": [
+        {
+            "dockerPull": "duplexa/4dn-repliseq:v9",
+            "class": "DockerRequirement"
+        }
+    ],
+    "arguments": [],
+    "class": "CommandLineTool",
+    "inputs": [
+        {
+            "type": [
+                "File"
+            ],
+            "id": "#input_bam",
+            "inputBinding": {
+                "position": 1,
+                "separate": true
+            }
+        },
+        {
+            "type": [
+                "null",
+                "string"
+            ],
+            "id": "#outprefix",
+            "inputBinding": {
+                "position": 3,
+                "separate": true
+            },
+            "default": "out"
+        },
+        {
+            "type": [
+                "null",
+                "string"
+            ],
+            "id": "#outdir",
+            "inputBinding": {
+                "position": 2,
+                "separate": true
+            },
+            "default": "."
+        }
+    ],
+    "outputs": [
+        {
+            "type": [
+                "null",
+                "File"
+            ],
+            "id": "#out_deduped_bam",
+            "outputBinding": {
+                "glob": "$(inputs.outdir + '/' + inputs.outprefix + '.rmdup.bam')"
+            }
+        },
+        {
+            "type": [
+                "null",
+                "File"
+            ],
+            "id": "#out_log",
+            "outputBinding": {
+                "glob": "$(inputs.outdir + '/' + inputs.outprefix + '.rmdup.bam.log')"
+            }
+        }
+    ],
+    "baseCommand": [
+        "dedup"
+    ],
+    "requirements": [
+        {
+            "class": "InlineJavascriptRequirement"
+        }
+    ],
+    "cwlVersion": "draft-3"
+}
diff --git a/cwl_awsem/repliseq/filter.cwl b/cwl_awsem/repliseq/filter.cwl
new file mode 100644
index 0000000..ba8ba52
--- /dev/null
+++ b/cwl_awsem/repliseq/filter.cwl
@@ -0,0 +1,77 @@
+{
+    "hints": [
+        {
+            "dockerPull": "duplexa/4dn-repliseq:v9",
+            "class": "DockerRequirement"
+        }
+    ],
+    "arguments": [],
+    "class": "CommandLineTool",
+    "inputs": [
+        {
+            "type": [
+                "File"
+            ],
+            "id": "#input_bg",
+            "inputBinding": {
+                "position": 1,
+                "separate": true
+            }
+        },
+        {
+            "type": [
+                "File"
+            ],
+            "id": "#filtered_bed",
+            "inputBinding": {
+                "position": 2,
+                "separate": true
+            }
+        },
+        {
+            "type": [
+                "null",
+                "string"
+            ],
+            "id": "#outprefix",
+            "inputBinding": {
+                "position": 4,
+                "separate": true
+            },
+            "default": "out"
+        },
+        {
+            "type": [
+                "null",
+                "string"
+            ],
+            "id": "#outdir",
+            "inputBinding": {
+                "position": 3,
+                "separate": true
+            },
+            "default": "."
+        }
+    ],
+    "outputs": [
+        {
+            "type": [
+                "null",
+                "File"
+            ],
+            "id": "#out_filtered_bg",
+            "outputBinding": {
+                "glob": "$(inputs.outdir + '/' + inputs.outprefix + '.filtered.bg')"
+            }
+        }
+    ],
+    "baseCommand": [
+        "filter"
+    ],
+    "requirements": [
+        {
+            "class": "InlineJavascriptRequirement"
+        }
+    ],
+    "cwlVersion": "draft-3"
+}
diff --git a/cwl_awsem/repliseq/filtersort.cwl b/cwl_awsem/repliseq/filtersort.cwl
new file mode 100644
index 0000000..d0419db
--- /dev/null
+++ b/cwl_awsem/repliseq/filtersort.cwl
@@ -0,0 +1,91 @@
+{
+    "hints": [
+        {
+            "dockerPull": "duplexa/4dn-repliseq:v9",
+            "class": "DockerRequirement"
+        }
+    ],
+    "arguments": [],
+    "class": "CommandLineTool",
+    "inputs": [
+        {
+            "type": [
+                "File"
+            ],
+            "id": "#input_bam",
+            "inputBinding": {
+                "position": 1,
+                "separate": true
+            }
+        },
+        {
+            "type": [
+                "null",
+                "int"
+            ],
+            "id": "#nextrathreads",
+            "inputBinding": {
+                "position": 3,
+                "separate": true
+            },
+            "default": 0
+        },
+        {
+            "type": [
+                "null",
+                "string"
+            ],
+            "id": "#memperthread",
+            "inputBinding": {
+                "position": 2,
+                "separate": true
+            },
+            "default": "5G"
+        },
+        {
+            "type": [
+                "null",
+                "string"
+            ],
+            "id": "#outprefix",
+            "inputBinding": {
+                "position": 5,
+                "separate": true
+            },
+            "default": "out"
+        },
+        {
+            "type": [
+                "null",
+                "string"
+            ],
+            "id": "#outdir",
+            "inputBinding": {
+                "position": 4,
+                "separate": true
+            },
+            "default": "."
+        }
+    ],
+    "outputs": [
+        {
+            "type": [
+                "null",
+                "File"
+            ],
+            "id": "#out_filtered_sorted_bam",
+            "outputBinding": {
+                "glob": "$(inputs.outdir + '/' + inputs.outprefix + '.q20_sort.bam')"
+            }
+        }
+    ],
+    "baseCommand": [
+        "filtersort"
+    ],
+    "requirements": [
+        {
+            "class": "InlineJavascriptRequirement"
+        }
+    ],
+    "cwlVersion": "draft-3"
+}
diff --git a/cwl_awsem/repliseq/log2ratio.cwl b/cwl_awsem/repliseq/log2ratio.cwl
new file mode 100644
index 0000000..187d472
--- /dev/null
+++ b/cwl_awsem/repliseq/log2ratio.cwl
@@ -0,0 +1,77 @@
+{
+    "hints": [
+        {
+            "dockerPull": "duplexa/4dn-repliseq:v9",
+            "class": "DockerRequirement"
+        }
+    ],
+    "arguments": [],
+    "class": "CommandLineTool",
+    "inputs": [
+        {
+            "type": [
+                "File"
+            ],
+            "id": "#input_ebg",
+            "inputBinding": {
+                "position": 1,
+                "separate": true
+            }
+        },
+        {
+            "type": [
+                "File"
+            ],
+            "id": "#input_lbg",
+            "inputBinding": {
+                "position": 2,
+                "separate": true
+            }
+        },
+        {
+            "type": [
+                "null",
+                "string"
+            ],
+            "id": "#outprefix",
+            "inputBinding": {
+                "position": 4,
+                "separate": true
+            },
+            "default": "out"
+        },
+        {
+            "type": [
+                "null",
+                "string"
+            ],
+            "id": "#outdir",
+            "inputBinding": {
+                "position": 3,
+                "separate": true
+            },
+            "default": "."
+        }
+    ],
+    "outputs": [
+        {
+            "type": [
+                "null",
+                "File"
+            ],
+            "id": "#out_log2ratio",
+            "outputBinding": {
+                "glob": "$(inputs.outdir + '/' + inputs.outprefix + '.l2r.out')"
+            }
+        }
+    ],
+    "baseCommand": [
+        "log2ratio"
+    ],
+    "requirements": [
+        {
+            "class": "InlineJavascriptRequirement"
+        }
+    ],
+    "cwlVersion": "draft-3"
+}
diff --git a/cwl_awsem/repliseq/make_filteredbed.cwl b/cwl_awsem/repliseq/make_filteredbed.cwl
new file mode 100644
index 0000000..540c6a6
--- /dev/null
+++ b/cwl_awsem/repliseq/make_filteredbed.cwl
@@ -0,0 +1,83 @@
+{
+    "outputs": [
+        {
+            "id": "#out_filtered_bed",
+            "type": [
+                "null",
+                "File"
+            ],
+            "outputBinding": {
+                "glob": "$(inputs.outdir + '/' + inputs.outprefix + '.filtered.bed')"
+            }
+        }
+    ],
+    "baseCommand": [
+        "make_filteredbed"
+    ],
+    "hints": [
+        {
+            "dockerPull": "duplexa/4dn-repliseq:v9",
+            "class": "DockerRequirement"
+        }
+    ],
+    "cwlVersion": "draft-3",
+    "class": "CommandLineTool",
+    "arguments": [],
+    "inputs": [
+        {
+            "id": "#outdir",
+            "inputBinding": {
+                "position": 1,
+                "separate": true
+            },
+            "default": ".",
+            "type": [
+                "null",
+                "string"
+            ]
+        },
+        {
+            "id": "#outprefix",
+            "inputBinding": {
+                "position": 2,
+                "separate": true
+            },
+            "default": "out",
+            "type": [
+                "null",
+                "string"
+            ]
+        },
+        {
+            "type": [
+                "float"
+            ],
+            "id": "#min_rpkm",
+            "inputBinding": {
+                "position": 3,
+                "separate": true
+            },
+            "default": 0.1
+        },
+        {
+            "id": "#input_bgs",
+            "inputBinding": {
+                "itemSeparator": " ",
+                "position": 4,
+                "separate": true
+            },
+            "type": [
+                "null",
+                {
+                    "items": "File",
+                    "type": "array"
+                }
+            ]
+        }
+    ],
+    "requirements": [
+        {
+            "class": "InlineJavascriptRequirement"
+        }
+    ]
+}
diff --git a/cwl_awsem/repliseq/make_referencebg.cwl b/cwl_awsem/repliseq/make_referencebg.cwl
new file mode 100644
index 0000000..d818c0b
--- /dev/null
+++ b/cwl_awsem/repliseq/make_referencebg.cwl
@@ -0,0 +1,72 @@
+{
+    "outputs": [
+        {
+            "id": "#out_reference_bg",
+            "type": [
+                "null",
+                "File"
+            ],
+            "outputBinding": {
+                "glob": "$(inputs.outdir + '/' + inputs.outprefix + '.inorm.bg')"
+            }
+        }
+    ],
+    "baseCommand": [
+        "make_referencebg"
+    ],
+    "hints": [
+        {
+            "dockerPull": "duplexa/4dn-repliseq:v9",
+            "class": "DockerRequirement"
+        }
+    ],
+    "cwlVersion": "draft-3",
+    "class": "CommandLineTool",
+    "arguments": [],
+    "inputs": [
+        {
+            "id": "#outdir",
+            "inputBinding": {
+                "position": 1,
+                "separate": true
+            },
+            "default": ".",
+            "type": [
+                "null",
+                "string"
+            ]
+        },
+        {
+            "id": "#outprefix",
+            "inputBinding": {
+                "position": 2,
+                "separate": true
+            },
+            "default": "out",
+            "type": [
+                "null",
+                "string"
+            ]
+        },
+        {
+            "id": "#input_bgs",
+            "inputBinding": {
+                "itemSeparator": " ",
+                "position": 3,
+                "separate": true
+            },
+            "type": [
+                "null",
+                {
+                    "items": "File",
+                    "type": "array"
+                }
+            ]
+        }
+    ],
+    "requirements": [
+        {
+            "class": "InlineJavascriptRequirement"
+        }
+    ]
+}
diff --git a/cwl_awsem/repliseq/normalize.cwl b/cwl_awsem/repliseq/normalize.cwl
new file mode 100644
index 0000000..673d0d1
--- /dev/null
+++ b/cwl_awsem/repliseq/normalize.cwl
@@ -0,0 +1,78 @@
+{
+    "hints": [
+        {
+            "dockerPull": "duplexa/4dn-repliseq:v9",
+            "class": "DockerRequirement"
+        }
+    ],
+    "arguments": [],
+    "class": "CommandLineTool",
+    "inputs": [
+        {
+            "type": [
+                "File"
+            ],
+            "id": "#input",
+            "inputBinding": {
+                "position": 1,
+                "separate": true
+            }
+        },
+        {
+            "type": [
+                "File",
+                "null"
+            ],
+            "id": "#reference_bg",
+            "inputBinding": {
+                "position": 2,
+                "separate": true
+            }
+        },
+        {
+            "type": [
+                "null",
+                "string"
+            ],
+            "id": "#outprefix",
+            "inputBinding": {
+                "position": 4,
+                "separate": true
+            },
+            "default": "out"
+        },
+        {
+            "type": [
+                "null",
+                "string"
+            ],
+            "id": "#outdir",
+            "inputBinding": {
+                "position": 3,
+                "separate": true
+            },
+            "default": "."
+        }
+    ],
+    "outputs": [
+        {
+            "type": [
+                "null",
+                "File"
+            ],
+            "id": "#out_norm_bg",
+            "outputBinding": {
+                "glob": "$(inputs.outdir + '/' + inputs.outprefix + '.qnorm.bg')"
+            }
+        }
+    ],
+    "baseCommand": [
+        "normalize"
+    ],
+    "requirements": [
+        {
+            "class": "InlineJavascriptRequirement"
+        }
+    ],
+    "cwlVersion": "draft-3"
+}
diff --git a/cwl_awsem/repliseq/smooth.cwl b/cwl_awsem/repliseq/smooth.cwl
new file mode 100644
index 0000000..b768fc1
--- /dev/null
+++ b/cwl_awsem/repliseq/smooth.cwl
@@ -0,0 +1,81 @@
+{
+    "hints": [
+        {
+            "dockerPull": "duplexa/4dn-repliseq:v9",
+            "class": "DockerRequirement"
+        }
+    ],
+    "arguments": [],
+    "class": "CommandLineTool",
+    "inputs": [
+        {
+            "type": [
+                "File"
+            ],
+            "id": "#input_bg",
+            "inputBinding": {
+                "position": 4,
+                "separate": true
+            }
+        },
+        {
+            "type": [
+                "int"
+            ],
+            "id": "#lspan",
+            "inputBinding": {
+                "position": 1,
+                "separate": true,
+                "prefix": '-l'
+            },
+            "default": 300000
+        },
+        {
+            "type": [
+                "null",
+                "string"
+            ],
+            "id": "#outprefix",
+            "inputBinding": {
+                "position": 3,
+                "separate": true,
+                "prefix": '-p'
+            },
+            "default": "out"
+        },
+        {
+            "type": [
+                "null",
+                "string"
+            ],
+            "id": "#outdir",
+            "inputBinding": {
+                "position": 2,
+                "separate": true,
+                "prefix": '-d'
+            },
+            "default": "."
+        }
+    ],
+    "outputs": [
+        {
+            "type": [
+                "null",
+                "File"
+            ],
+            "id": "#out_smooth_bg",
+            "outputBinding": {
+                "glob": "$(inputs.outdir + '/' + inputs.outprefix + '.loess' + inputs.lspan + '.bg')"
+            }
+        }
+    ],
+    "baseCommand": [
+        "smooth"
+    ],
+    "requirements": [
+        {
+            "class": "InlineJavascriptRequirement"
+        }
+    ],
+    "cwlVersion": "draft-3"
+}