Merge pull request #30 from alexbarrera/master

Upgrade workflows to CWL v1.0
Duke-GCB · Apr 18, 2018 · c269cec · c269cec
2 parents cd3a09c + c32207c
commit c269cec
Show file tree

Hide file tree

Showing 400 changed files with 25,394 additions and 81 deletions.
diff --git a/.gitmodules b/.gitmodules
@@ -1,4 +1,4 @@
 [submodule "workflows"]
 	path = workflows
 	url = https://github.com/alexbarrera/workflows
-	branch = draft-3
+	branch = v1.0
diff --git a/README.md b/README.md
@@ -4,119 +4,113 @@
 
 CWL tools and workflows associated with the Genomics of Gene Regulation (GGR) project
 
-GGR pipelines created using the [Common Workflow Language](http://www.commonwl.org/) `draft-3` specification. 
+GGR pipelines created using the [Common Workflow Language](http://www.commonwl.org/) `v1.0` specification. 
 The workflows are parametrized with values that best suit the GGR samples, but they can be easily tailored for specific needs.
 
 For a detail User Guide to the CWL workflows, please see the [wiki](https://github.com/Duke-GCB/GGR-cwl/wiki).
 
-## [ChIP-seq](ChIP-seq_pipeline):
+## [ChIP-seq](v1.0/ChIP-seq_pipeline):
 
 ### Pipelines
-* [SE - Narrow](ChIP-seq_pipeline/pipeline-se-narrow.cwl)
-* [SE - Narrow - w/control](ChIP-seq_pipeline/pipeline-se-narrow-with-control.cwl)
-* [SE - Broad](ChIP-seq_pipeline/pipeline-se-broad.cwl)
-* [SE - Broad - w/control](ChIP-seq_pipeline/pipeline-se-broad-with-control.cwl)
-* [PE - Narrow](ChIP-seq_pipeline/pipeline-pe-narrow.cwl)
-* [PE - Narrow - w/control](ChIP-seq_pipeline/pipeline-pe-narrow-with-control.cwl)
-* [PE - Broad](ChIP-seq_pipeline/pipeline-pe-broad.cwl)
-* [PE - Broad - w/control](ChIP-seq_pipeline/pipeline-pe-broad-with-control.cwl)
+* [SE](v1.0/ChIP-seq_pipeline/pipeline-se.cwl)
+* [SE - w/control](v1.0/ChIP-seq_pipeline/pipeline-se-with-control.cwl)
+* [PE](v1.0/ChIP-seq_pipeline/pipeline-pe.cwl)
+* [PE - w/control](v1.0/ChIP-seq_pipeline/pipeline-pe-with-control.cwl)
 
 ### Steps
 * 01 - Fastq QC step:
-    * [Fastq QC step - SE](ChIP-seq_pipeline/01-qc-se.cwl)
-    * [Fastq QC step - PE](ChIP-seq_pipeline/01-qc-pe.cwl)
+    * [Fastq QC step - SE](v1.0/ChIP-seq_pipeline/01-qc-se.cwl)
+    * [Fastq QC step - PE](v1.0/ChIP-seq_pipeline/01-qc-pe.cwl)
 * 02 - Trimming reads step:
-    * [Trimming step - SE](ChIP-seq_pipeline/02-trim-se.cwl)
-    * [Trimming step - PE](ChIP-seq_pipeline/02-trim-pe.cwl)
+    * [Trimming step - SE](v1.0/ChIP-seq_pipeline/02-trim-se.cwl)
+    * [Trimming step - PE](v1.0/ChIP-seq_pipeline/02-trim-pe.cwl)
 * 03 - Mapping step:
-    * [Mapping step - SE](ChIP-seq_pipeline/03-map-se.cwl)
-    * [Mapping step - PE](ChIP-seq_pipeline/03-map-pe.cwl)
+    * [Mapping step - SE](v1.0/ChIP-seq_pipeline/03-map-se.cwl)
+    * [Mapping step - PE](v1.0/ChIP-seq_pipeline/03-map-pe.cwl)
 * 04 - Peak calling step:
-    * [Peak calling step - narrow](ChIP-seq_pipeline/04-peakcall-narrow.cwl)
-    * [Peak calling step - narrow with control](ChIP-seq_pipeline/04-peakcall-narrow-with-control.cwl)
-    * [Peak calling step - broad](ChIP-seq_pipeline/04-peakcall-broad.cwl)
-    * [Peak calling step - broad with control](ChIP-seq_pipeline/04-peakcall-broad-with-control.cwl)
+    * [Peak calling step](v1.0/ChIP-seq_pipeline/04-peakcall.cwl)
+    * [Peak calling step - with control](v1.0/ChIP-seq_pipeline/04-peakcall-with-control.cwl)
 * 05 - Quantification step:
-    * [Quantification step](ChIP-seq_pipeline/05-quantification.cwl)
-    * [Quantification step - with control](ChIP-seq_pipeline/05-quantification-with-control.cwl)
+    * [Quantification step](v1.0/ChIP-seq_pipeline/05-quantification.cwl)
+    * [Quantification step - with control](v1.0/ChIP-seq_pipeline/05-quantification-with-control.cwl)
 
-## [DNase-seq](DNase-seq_pipeline):
+## [DNase-seq](v1.0/DNase-seq_pipeline):
 
 ### Pipelines
-* [SE](DNase-seq_pipeline/pipeline-se.cwl)
+* [SE](v1.0/DNase-seq_pipeline/pipeline-se.cwl)
 
 ### Steps
 * 01 - Mapping step:
-    * 01 - [Mapping step - SE](DNase-seq_pipeline/01-map-se.cwl)
+    * 01 - [Mapping step - SE](v1.0/DNase-seq_pipeline/01-map-se.cwl)
 * 02 - Peak calling step:
-    * 02 - [Peak calling step](DNase-seq_pipeline/02-peakcall.cwl)
+    * 02 - [Peak calling step](v1.0/DNase-seq_pipeline/02-peakcall.cwl)
 * 03 - Quantification step:
-    * 03 - [Quantification step](DNase-seq_pipeline/03-quantification.cwl)
+    * 03 - [Quantification step](v1.0/DNase-seq_pipeline/03-quantification.cwl)
 
 
-## [RNA-seq](RNA-seq_pipeline):
+## [RNA-seq](v1.0/RNA-seq_pipeline):
 
 ### Pipelines
-* [SE - Unstranded](RNA-seq_pipeline/pipeline-se-unstranded.cwl)
-* [SE - Unstranded - w/sjdb](RNA-seq_pipeline/pipeline-se-unstranded-with-sjdb.cwl)
-* [SE - Stranded](RNA-seq_pipeline/pipeline-se-stranded.cwl)
-* [SE - Stranded - w/sjdb](RNA-seq_pipeline/pipeline-se-stranded-with-sjdb.cwl)
-* [SE - Revstranded](RNA-seq_pipeline/pipeline-se-revstranded.cwl)
-* [SE - Revstranded - w/sjdb](RNA-seq_pipeline/pipeline-se-revstranded-with-sjdb.cwl)
-* [PE - Unstranded](RNA-seq_pipeline/pipeline-pe-unstranded.cwl)
-* [PE - Unstranded - w/sjdb](RNA-seq_pipeline/pipeline-pe-unstranded-with-sjdb.cwl)
-* [PE - Stranded](RNA-seq_pipeline/pipeline-pe-stranded.cwl)
-* [PE - Stranded - w/sjdb](RNA-seq_pipeline/pipeline-pe-stranded-with-sjdb.cwl)
-* [PE - Revstranded](RNA-seq_pipeline/pipeline-pe-revstranded.cwl)
-* [PE - Revstranded - w/sjdb](RNA-seq_pipeline/pipeline-pe-revstranded-with-sjdb.cwl)
+* [SE - Unstranded](v1.0/RNA-seq_pipeline/pipeline-se-unstranded.cwl)
+* [SE - Unstranded - w/sjdb](v1.0/RNA-seq_pipeline/pipeline-se-unstranded-with-sjdb.cwl)
+* [SE - Stranded](v1.0/RNA-seq_pipeline/pipeline-se-stranded.cwl)
+* [SE - Stranded - w/sjdb](v1.0/RNA-seq_pipeline/pipeline-se-stranded-with-sjdb.cwl)
+* [SE - Revstranded](v1.0/RNA-seq_pipeline/pipeline-se-revstranded.cwl)
+* [SE - Revstranded - w/sjdb](v1.0/RNA-seq_pipeline/pipeline-se-revstranded-with-sjdb.cwl)
+* [PE - Unstranded](v1.0/RNA-seq_pipeline/pipeline-pe-unstranded.cwl)
+* [PE - Unstranded - w/sjdb](v1.0/RNA-seq_pipeline/pipeline-pe-unstranded-with-sjdb.cwl)
+* [PE - Stranded](v1.0/RNA-seq_pipeline/pipeline-pe-stranded.cwl)
+* [PE - Stranded - w/sjdb](v1.0/RNA-seq_pipeline/pipeline-pe-stranded-with-sjdb.cwl)
+* [PE - Revstranded](v1.0/RNA-seq_pipeline/pipeline-pe-revstranded.cwl)
+* [PE - Revstranded - w/sjdb](v1.0/RNA-seq_pipeline/pipeline-pe-revstranded-with-sjdb.cwl)
 
 ### Steps
 * 00 - Genome files generation for STAR and RSEM:
-    * 00 - [Preprocessing step](RNA-seq_pipeline/00-preprocessing.cwl)
+    * 00 - [Preprocessing step](v1.0/RNA-seq_pipeline/00-preprocessing.cwl)
 * 01 - Fastq QC step:
-    * 01 - [Fastq QC step - SE](RNA-seq_pipeline/01-qc-se.cwl)
-    * 01 - [Fastq QC step - PE](RNA-seq_pipeline/01-qc-pe.cwl)
+    * 01 - [Fastq QC step - SE](v1.0/RNA-seq_pipeline/01-qc-se.cwl)
+    * 01 - [Fastq QC step - PE](v1.0/RNA-seq_pipeline/01-qc-pe.cwl)
 * 02 - Trimming reads step:
-    * 02 - [Trimming step - SE](RNA-seq_pipeline/02-trim-se.cwl)
-    * 02 - [Trimming step - PE](RNA-seq_pipeline/02-trim-pe.cwl)
+    * 02 - [Trimming step - SE](v1.0/RNA-seq_pipeline/02-trim-se.cwl)
+    * 02 - [Trimming step - PE](v1.0/RNA-seq_pipeline/02-trim-pe.cwl)
 * 03 - Mapping step:
-    * 03 - [Mapping step - SE](RNA-seq_pipeline/03-map-se.cwl)
-    * 03 - [Mapping step - SE - w/sjdb](RNA-seq_pipeline/03-map-se-with-sjdb.cwl)
-    * 03 - [Mapping step - PE](RNA-seq_pipeline/03-map-pe.cwl)
-    * 03 - [Mapping step - PE - w/sjdb](RNA-seq_pipeline/03-map-pe-with-sjdb.cwl)
+    * 03 - [Mapping step - SE](v1.0/RNA-seq_pipeline/03-map-se.cwl)
+    * 03 - [Mapping step - SE - w/sjdb](v1.0/RNA-seq_pipeline/03-map-se-with-sjdb.cwl)
+    * 03 - [Mapping step - PE](v1.0/RNA-seq_pipeline/03-map-pe.cwl)
+    * 03 - [Mapping step - PE - w/sjdb](v1.0/RNA-seq_pipeline/03-map-pe-with-sjdb.cwl)
 * 04 - Quantification step:
-    * 04 - [Quantification step - SE - Unstranded](RNA-seq_pipeline/04-quantification-se-unstranded.cwl)
-    * 04 - [Quantification step - SE - Stranded](RNA-seq_pipeline/04-quantification-se-stranded.cwl)
-    * 04 - [Quantification step - SE - Revstranded](RNA-seq_pipeline/04-quantification-se-revstranded.cwl)
-    * 04 - [Quantification step - PE - Unstranded](RNA-seq_pipeline/04-quantification-pe-unstranded.cwl)
-    * 04 - [Quantification step - PE - Stranded](RNA-seq_pipeline/04-quantification-pe-stranded.cwl)
-    * 04 - [Quantification step - PE - Revstranded](RNA-seq_pipeline/04-quantification-pe-revstranded.cwl)
+    * 04 - [Quantification step - SE - Unstranded](v1.0/RNA-seq_pipeline/04-quantification-se-unstranded.cwl)
+    * 04 - [Quantification step - SE - Stranded](v1.0/RNA-seq_pipeline/04-quantification-se-stranded.cwl)
+    * 04 - [Quantification step - SE - Revstranded](v1.0/RNA-seq_pipeline/04-quantification-se-revstranded.cwl)
+    * 04 - [Quantification step - PE - Unstranded](v1.0/RNA-seq_pipeline/04-quantification-pe-unstranded.cwl)
+    * 04 - [Quantification step - PE - Stranded](v1.0/RNA-seq_pipeline/04-quantification-pe-stranded.cwl)
+    * 04 - [Quantification step - PE - Revstranded](v1.0/RNA-seq_pipeline/04-quantification-pe-revstranded.cwl)
 
-## [ATAC-seq](ATAC-seq_pipeline):
+## [ATAC-seq](v1.0/ATAC-seq_pipeline):
 
 ### Pipelines
-* [SE](ATAC-seq_pipeline/pipeline-se.cwl)
-* [SE - Blacklist Removal](ATAC-seq_pipeline/pipeline-se-blacklist-removal.cwl)
-* [PE](ATAC-seq_pipeline/pipeline-pe.cwl)
-* [PE - Blacklist Removal](ATAC-seq_pipeline/pipeline-pe-blacklist-removal.cwl)
+* [SE](v1.0/ATAC-seq_pipeline/pipeline-se.cwl)
+* [SE - Blacklist Removal](v1.0/ATAC-seq_pipeline/pipeline-se-blacklist-removal.cwl)
+* [PE](v1.0/ATAC-seq_pipeline/pipeline-pe.cwl)
+* [PE - Blacklist Removal](v1.0/ATAC-seq_pipeline/pipeline-pe-blacklist-removal.cwl)
 
 ### Steps
 * 01 - Fastq QC step:
-    * [Fastq QC step - SE](ATAC-seq_pipeline/01-qc-se.cwl)
-    * [Fastq QC step - PE](ATAC-seq_pipeline/01-qc-pe.cwl)
+    * [Fastq QC step - SE](v1.0/ATAC-seq_pipeline/01-qc-se.cwl)
+    * [Fastq QC step - PE](v1.0/ATAC-seq_pipeline/01-qc-pe.cwl)
 * 02 - Trimming reads step:
-    * [Trimming step - SE](ATAC-seq_pipeline/02-trim-se.cwl)
-    * [Trimming step - PE](ATAC-seq_pipeline/02-trim-pe.cwl)
+    * [Trimming step - SE](v1.0/ATAC-seq_pipeline/02-trim-se.cwl)
+    * [Trimming step - PE](v1.0/ATAC-seq_pipeline/02-trim-pe.cwl)
 * 03 - Mapping step:
-    * [Mapping step - SE](ATAC-seq_pipeline/03-map-se.cwl)
-    * [Mapping step - SE - Blacklist Removal](ATAC-seq_pipeline/03-map-se-blacklist-removal.cwl)
-    * [Mapping step - PE](ATAC-seq_pipeline/03-map-pe.cwl)
-    * [Mapping step - PE - Blacklist Removal](ATAC-seq_pipeline/03-map-pe-blacklist-removal.cwl)
+    * [Mapping step - SE](v1.0/ATAC-seq_pipeline/03-map-se.cwl)
+    * [Mapping step - SE - Blacklist Removal](v1.0/ATAC-seq_pipeline/03-map-se-blacklist-removal.cwl)
+    * [Mapping step - PE](v1.0/ATAC-seq_pipeline/03-map-pe.cwl)
+    * [Mapping step - PE - Blacklist Removal](v1.0/ATAC-seq_pipeline/03-map-pe-blacklist-removal.cwl)
 * 04 - Peak calling step:
-    * [Peak calling step - SE](ATAC-seq_pipeline/04-peakcall-se.cwl)
-    * [Peak calling step - PE](ATAC-seq_pipeline/04-peakcall-pe.cwl)
+    * [Peak calling step - SE](v1.0/ATAC-seq_pipeline/04-peakcall-se.cwl)
+    * [Peak calling step - PE](v1.0/ATAC-seq_pipeline/04-peakcall-pe.cwl)
 * 05 - Quantification step:
-    * [Quantification step](ATAC-seq_pipeline/05-quantification.cwl)
+    * [Quantification step](v1.0/ATAC-seq_pipeline/05-quantification.cwl)
 
 
 ----------------------------------------------------------------------------------------------------------
@@ -127,10 +121,6 @@ Depending on the experiments, there might be small differences in the workflows
     - Type of read:
         - SE: Single End reads
         - PE: Paired-End reads
-- ChIP-seq & DNase-seq
-    - Type of region targeted:
-        - Narrow: Narrow (also known as Point-Source) peaks. Limited region bound (e.g. TFs).
-        - Broad: Broad peaks. Wide region bound (e.g. Histone modifications)
 - ChIP-seq only
     - With or without control. If a control sample is available `-with-control` or not.
 - RNA-seq only

diff --git a/ATAC-seq_pipeline/01-qc-pe.cwl → draft-3/ATAC-seq_pipeline/01-qc-pe.cwl b/ATAC-seq_pipeline/01-qc-pe.cwl → draft-3/ATAC-seq_pipeline/01-qc-pe.cwl
diff --git a/ATAC-seq_pipeline/01-qc-se.cwl → draft-3/ATAC-seq_pipeline/01-qc-se.cwl b/ATAC-seq_pipeline/01-qc-se.cwl → draft-3/ATAC-seq_pipeline/01-qc-se.cwl
diff --git a/ATAC-seq_pipeline/02-trim-pe.cwl → draft-3/ATAC-seq_pipeline/02-trim-pe.cwl b/ATAC-seq_pipeline/02-trim-pe.cwl → draft-3/ATAC-seq_pipeline/02-trim-pe.cwl
diff --git a/ATAC-seq_pipeline/02-trim-se.cwl → draft-3/ATAC-seq_pipeline/02-trim-se.cwl b/ATAC-seq_pipeline/02-trim-se.cwl → draft-3/ATAC-seq_pipeline/02-trim-se.cwl
diff --git a/..._pipeline/03-map-pe-blacklist-removal.cwl → ..._pipeline/03-map-pe-blacklist-removal.cwl b/..._pipeline/03-map-pe-blacklist-removal.cwl → ..._pipeline/03-map-pe-blacklist-removal.cwl
diff --git a/ATAC-seq_pipeline/03-map-pe.cwl → draft-3/ATAC-seq_pipeline/03-map-pe.cwl b/ATAC-seq_pipeline/03-map-pe.cwl → draft-3/ATAC-seq_pipeline/03-map-pe.cwl
diff --git a/..._pipeline/03-map-se-blacklist-removal.cwl → ..._pipeline/03-map-se-blacklist-removal.cwl b/..._pipeline/03-map-se-blacklist-removal.cwl → ..._pipeline/03-map-se-blacklist-removal.cwl
diff --git a/ATAC-seq_pipeline/03-map-se.cwl → draft-3/ATAC-seq_pipeline/03-map-se.cwl b/ATAC-seq_pipeline/03-map-se.cwl → draft-3/ATAC-seq_pipeline/03-map-se.cwl
diff --git a/ATAC-seq_pipeline/04-peakcall-pe.cwl → draft-3/ATAC-seq_pipeline/04-peakcall-pe.cwl b/ATAC-seq_pipeline/04-peakcall-pe.cwl → draft-3/ATAC-seq_pipeline/04-peakcall-pe.cwl
diff --git a/ATAC-seq_pipeline/04-peakcall-se.cwl → draft-3/ATAC-seq_pipeline/04-peakcall-se.cwl b/ATAC-seq_pipeline/04-peakcall-se.cwl → draft-3/ATAC-seq_pipeline/04-peakcall-se.cwl
diff --git a/ATAC-seq_pipeline/05-quantification.cwl → ...3/ATAC-seq_pipeline/05-quantification.cwl b/ATAC-seq_pipeline/05-quantification.cwl → ...3/ATAC-seq_pipeline/05-quantification.cwl
diff --git a/...ipeline/pipeline-pe-blacklist-removal.cwl → ...ipeline/pipeline-pe-blacklist-removal.cwl b/...ipeline/pipeline-pe-blacklist-removal.cwl → ...ipeline/pipeline-pe-blacklist-removal.cwl
diff --git a/ATAC-seq_pipeline/pipeline-pe.cwl → draft-3/ATAC-seq_pipeline/pipeline-pe.cwl b/ATAC-seq_pipeline/pipeline-pe.cwl → draft-3/ATAC-seq_pipeline/pipeline-pe.cwl
diff --git a/...ipeline/pipeline-se-blacklist-removal.cwl → ...ipeline/pipeline-se-blacklist-removal.cwl b/...ipeline/pipeline-se-blacklist-removal.cwl → ...ipeline/pipeline-se-blacklist-removal.cwl
diff --git a/ATAC-seq_pipeline/pipeline-se.cwl → draft-3/ATAC-seq_pipeline/pipeline-se.cwl b/ATAC-seq_pipeline/pipeline-se.cwl → draft-3/ATAC-seq_pipeline/pipeline-se.cwl
diff --git a/ChIP-seq_pipeline/01-qc-pe.cwl → draft-3/ChIP-seq_pipeline/01-qc-pe.cwl b/ChIP-seq_pipeline/01-qc-pe.cwl → draft-3/ChIP-seq_pipeline/01-qc-pe.cwl
diff --git a/ChIP-seq_pipeline/01-qc-se.cwl → draft-3/ChIP-seq_pipeline/01-qc-se.cwl b/ChIP-seq_pipeline/01-qc-se.cwl → draft-3/ChIP-seq_pipeline/01-qc-se.cwl
diff --git a/ChIP-seq_pipeline/02-trim-pe.cwl → draft-3/ChIP-seq_pipeline/02-trim-pe.cwl b/ChIP-seq_pipeline/02-trim-pe.cwl → draft-3/ChIP-seq_pipeline/02-trim-pe.cwl
diff --git a/ChIP-seq_pipeline/02-trim-se.cwl → draft-3/ChIP-seq_pipeline/02-trim-se.cwl b/ChIP-seq_pipeline/02-trim-se.cwl → draft-3/ChIP-seq_pipeline/02-trim-se.cwl
diff --git a/ChIP-seq_pipeline/03-map-pe.cwl → draft-3/ChIP-seq_pipeline/03-map-pe.cwl b/ChIP-seq_pipeline/03-map-pe.cwl → draft-3/ChIP-seq_pipeline/03-map-pe.cwl
diff --git a/ChIP-seq_pipeline/03-map-se.cwl → draft-3/ChIP-seq_pipeline/03-map-se.cwl b/ChIP-seq_pipeline/03-map-se.cwl → draft-3/ChIP-seq_pipeline/03-map-se.cwl
diff --git a/...peline/04-peakcall-broad-with-control.cwl → ...peline/04-peakcall-broad-with-control.cwl b/...peline/04-peakcall-broad-with-control.cwl → ...peline/04-peakcall-broad-with-control.cwl
diff --git a/ChIP-seq_pipeline/04-peakcall-broad.cwl → ...3/ChIP-seq_pipeline/04-peakcall-broad.cwl b/ChIP-seq_pipeline/04-peakcall-broad.cwl → ...3/ChIP-seq_pipeline/04-peakcall-broad.cwl
diff --git a/...eline/04-peakcall-narrow-with-control.cwl → ...eline/04-peakcall-narrow-with-control.cwl b/...eline/04-peakcall-narrow-with-control.cwl → ...eline/04-peakcall-narrow-with-control.cwl
diff --git a/ChIP-seq_pipeline/04-peakcall-narrow.cwl → .../ChIP-seq_pipeline/04-peakcall-narrow.cwl b/ChIP-seq_pipeline/04-peakcall-narrow.cwl → .../ChIP-seq_pipeline/04-peakcall-narrow.cwl
diff --git a/...peline/05-quantification-with-control.cwl → ...peline/05-quantification-with-control.cwl b/...peline/05-quantification-with-control.cwl → ...peline/05-quantification-with-control.cwl
diff --git a/ChIP-seq_pipeline/05-quantification.cwl → ...3/ChIP-seq_pipeline/05-quantification.cwl b/ChIP-seq_pipeline/05-quantification.cwl → ...3/ChIP-seq_pipeline/05-quantification.cwl
diff --git a/...peline/pipeline-pe-broad-with-control.cwl → ...peline/pipeline-pe-broad-with-control.cwl b/...peline/pipeline-pe-broad-with-control.cwl → ...peline/pipeline-pe-broad-with-control.cwl
diff --git a/ChIP-seq_pipeline/pipeline-pe-broad.cwl → ...3/ChIP-seq_pipeline/pipeline-pe-broad.cwl b/ChIP-seq_pipeline/pipeline-pe-broad.cwl → ...3/ChIP-seq_pipeline/pipeline-pe-broad.cwl
diff --git a/...eline/pipeline-pe-narrow-with-control.cwl → ...eline/pipeline-pe-narrow-with-control.cwl b/...eline/pipeline-pe-narrow-with-control.cwl → ...eline/pipeline-pe-narrow-with-control.cwl
diff --git a/ChIP-seq_pipeline/pipeline-pe-narrow.cwl → .../ChIP-seq_pipeline/pipeline-pe-narrow.cwl b/ChIP-seq_pipeline/pipeline-pe-narrow.cwl → .../ChIP-seq_pipeline/pipeline-pe-narrow.cwl
diff --git a/...peline/pipeline-se-broad-with-control.cwl → ...peline/pipeline-se-broad-with-control.cwl b/...peline/pipeline-se-broad-with-control.cwl → ...peline/pipeline-se-broad-with-control.cwl
diff --git a/ChIP-seq_pipeline/pipeline-se-broad.cwl → ...3/ChIP-seq_pipeline/pipeline-se-broad.cwl b/ChIP-seq_pipeline/pipeline-se-broad.cwl → ...3/ChIP-seq_pipeline/pipeline-se-broad.cwl
diff --git a/...eline/pipeline-se-narrow-with-control.cwl → ...eline/pipeline-se-narrow-with-control.cwl b/...eline/pipeline-se-narrow-with-control.cwl → ...eline/pipeline-se-narrow-with-control.cwl
diff --git a/ChIP-seq_pipeline/pipeline-se-narrow.cwl → .../ChIP-seq_pipeline/pipeline-se-narrow.cwl b/ChIP-seq_pipeline/pipeline-se-narrow.cwl → .../ChIP-seq_pipeline/pipeline-se-narrow.cwl
diff --git a/DNase-seq_pipeline/01-map-se.cwl → draft-3/DNase-seq_pipeline/01-map-se.cwl b/DNase-seq_pipeline/01-map-se.cwl → draft-3/DNase-seq_pipeline/01-map-se.cwl
diff --git a/DNase-seq_pipeline/02-peakcall.cwl → draft-3/DNase-seq_pipeline/02-peakcall.cwl b/DNase-seq_pipeline/02-peakcall.cwl → draft-3/DNase-seq_pipeline/02-peakcall.cwl
diff --git a/DNase-seq_pipeline/03-quantification.cwl → .../DNase-seq_pipeline/03-quantification.cwl b/DNase-seq_pipeline/03-quantification.cwl → .../DNase-seq_pipeline/03-quantification.cwl
diff --git a/DNase-seq_pipeline/pipeline-se.cwl → draft-3/DNase-seq_pipeline/pipeline-se.cwl b/DNase-seq_pipeline/pipeline-se.cwl → draft-3/DNase-seq_pipeline/pipeline-se.cwl
diff --git a/RNA-seq_pipeline/00-preprocessing.cwl → ...t-3/RNA-seq_pipeline/00-preprocessing.cwl b/RNA-seq_pipeline/00-preprocessing.cwl → ...t-3/RNA-seq_pipeline/00-preprocessing.cwl
diff --git a/RNA-seq_pipeline/01-qc-pe.cwl → draft-3/RNA-seq_pipeline/01-qc-pe.cwl b/RNA-seq_pipeline/01-qc-pe.cwl → draft-3/RNA-seq_pipeline/01-qc-pe.cwl
diff --git a/RNA-seq_pipeline/01-qc-se.cwl → draft-3/RNA-seq_pipeline/01-qc-se.cwl b/RNA-seq_pipeline/01-qc-se.cwl → draft-3/RNA-seq_pipeline/01-qc-se.cwl
diff --git a/RNA-seq_pipeline/02-trim-pe.cwl → draft-3/RNA-seq_pipeline/02-trim-pe.cwl b/RNA-seq_pipeline/02-trim-pe.cwl → draft-3/RNA-seq_pipeline/02-trim-pe.cwl
diff --git a/RNA-seq_pipeline/02-trim-se.cwl → draft-3/RNA-seq_pipeline/02-trim-se.cwl b/RNA-seq_pipeline/02-trim-se.cwl → draft-3/RNA-seq_pipeline/02-trim-se.cwl
diff --git a/RNA-seq_pipeline/03-map-pe-with-sjdb.cwl → .../RNA-seq_pipeline/03-map-pe-with-sjdb.cwl b/RNA-seq_pipeline/03-map-pe-with-sjdb.cwl → .../RNA-seq_pipeline/03-map-pe-with-sjdb.cwl
diff --git a/RNA-seq_pipeline/03-map-pe.cwl → draft-3/RNA-seq_pipeline/03-map-pe.cwl b/RNA-seq_pipeline/03-map-pe.cwl → draft-3/RNA-seq_pipeline/03-map-pe.cwl
diff --git a/RNA-seq_pipeline/03-map-se-with-sjdb.cwl → .../RNA-seq_pipeline/03-map-se-with-sjdb.cwl b/RNA-seq_pipeline/03-map-se-with-sjdb.cwl → .../RNA-seq_pipeline/03-map-se-with-sjdb.cwl
diff --git a/RNA-seq_pipeline/03-map-se.cwl → draft-3/RNA-seq_pipeline/03-map-se.cwl b/RNA-seq_pipeline/03-map-se.cwl → draft-3/RNA-seq_pipeline/03-map-se.cwl
diff --git a/...line/04-quantification-pe-revstranded.cwl → ...line/04-quantification-pe-revstranded.cwl b/...line/04-quantification-pe-revstranded.cwl → ...line/04-quantification-pe-revstranded.cwl
diff --git a/...ipeline/04-quantification-pe-stranded.cwl → ...ipeline/04-quantification-pe-stranded.cwl b/...ipeline/04-quantification-pe-stranded.cwl → ...ipeline/04-quantification-pe-stranded.cwl
diff --git a/...eline/04-quantification-pe-unstranded.cwl → ...eline/04-quantification-pe-unstranded.cwl b/...eline/04-quantification-pe-unstranded.cwl → ...eline/04-quantification-pe-unstranded.cwl
diff --git a/...line/04-quantification-se-revstranded.cwl → ...line/04-quantification-se-revstranded.cwl b/...line/04-quantification-se-revstranded.cwl → ...line/04-quantification-se-revstranded.cwl
diff --git a/...ipeline/04-quantification-se-stranded.cwl → ...ipeline/04-quantification-se-stranded.cwl b/...ipeline/04-quantification-se-stranded.cwl → ...ipeline/04-quantification-se-stranded.cwl
diff --git a/...eline/04-quantification-se-unstranded.cwl → ...eline/04-quantification-se-unstranded.cwl b/...eline/04-quantification-se-unstranded.cwl → ...eline/04-quantification-se-unstranded.cwl
diff --git a/...ine/pipeline-pe-revstranded-with-sjdb.cwl → ...ine/pipeline-pe-revstranded-with-sjdb.cwl b/...ine/pipeline-pe-revstranded-with-sjdb.cwl → ...ine/pipeline-pe-revstranded-with-sjdb.cwl
diff --git a/RNA-seq_pipeline/pipeline-pe-revstranded.cwl → ...-seq_pipeline/pipeline-pe-revstranded.cwl b/RNA-seq_pipeline/pipeline-pe-revstranded.cwl → ...-seq_pipeline/pipeline-pe-revstranded.cwl
diff --git a/...peline/pipeline-pe-stranded-with-sjdb.cwl → ...peline/pipeline-pe-stranded-with-sjdb.cwl b/...peline/pipeline-pe-stranded-with-sjdb.cwl → ...peline/pipeline-pe-stranded-with-sjdb.cwl
diff --git a/RNA-seq_pipeline/pipeline-pe-stranded.cwl → ...RNA-seq_pipeline/pipeline-pe-stranded.cwl b/RNA-seq_pipeline/pipeline-pe-stranded.cwl → ...RNA-seq_pipeline/pipeline-pe-stranded.cwl
diff --git a/...line/pipeline-pe-unstranded-with-sjdb.cwl → ...line/pipeline-pe-unstranded-with-sjdb.cwl b/...line/pipeline-pe-unstranded-with-sjdb.cwl → ...line/pipeline-pe-unstranded-with-sjdb.cwl
diff --git a/RNA-seq_pipeline/pipeline-pe-unstranded.cwl → ...A-seq_pipeline/pipeline-pe-unstranded.cwl b/RNA-seq_pipeline/pipeline-pe-unstranded.cwl → ...A-seq_pipeline/pipeline-pe-unstranded.cwl
diff --git a/...ine/pipeline-se-revstranded-with-sjdb.cwl → ...ine/pipeline-se-revstranded-with-sjdb.cwl b/...ine/pipeline-se-revstranded-with-sjdb.cwl → ...ine/pipeline-se-revstranded-with-sjdb.cwl
diff --git a/RNA-seq_pipeline/pipeline-se-revstranded.cwl → ...-seq_pipeline/pipeline-se-revstranded.cwl b/RNA-seq_pipeline/pipeline-se-revstranded.cwl → ...-seq_pipeline/pipeline-se-revstranded.cwl
diff --git a/...peline/pipeline-se-stranded-with-sjdb.cwl → ...peline/pipeline-se-stranded-with-sjdb.cwl b/...peline/pipeline-se-stranded-with-sjdb.cwl → ...peline/pipeline-se-stranded-with-sjdb.cwl
diff --git a/RNA-seq_pipeline/pipeline-se-stranded.cwl → ...RNA-seq_pipeline/pipeline-se-stranded.cwl b/RNA-seq_pipeline/pipeline-se-stranded.cwl → ...RNA-seq_pipeline/pipeline-se-stranded.cwl
diff --git a/...line/pipeline-se-unstranded-with-sjdb.cwl → ...line/pipeline-se-unstranded-with-sjdb.cwl b/...line/pipeline-se-unstranded-with-sjdb.cwl → ...line/pipeline-se-unstranded-with-sjdb.cwl
diff --git a/RNA-seq_pipeline/pipeline-se-unstranded.cwl → ...A-seq_pipeline/pipeline-se-unstranded.cwl b/RNA-seq_pipeline/pipeline-se-unstranded.cwl → ...A-seq_pipeline/pipeline-se-unstranded.cwl
diff --git a/json-generator/__init__.py → draft-3/json-generator/__init__.py b/json-generator/__init__.py → draft-3/json-generator/__init__.py
diff --git a/json-generator/consts.py → draft-3/json-generator/consts.py b/json-generator/consts.py → draft-3/json-generator/consts.py
diff --git a/...atac_seq_Lerchter_3153_160217A3-se-0.json → ...atac_seq_Lerchter_3153_160217A3-se-0.json b/...atac_seq_Lerchter_3153_160217A3-se-0.json → ...atac_seq_Lerchter_3153_160217A3-se-0.json
diff --git a/...atac_seq_Lerchter_3153_160217A3-se-1.json → ...atac_seq_Lerchter_3153_160217A3-se-1.json b/...atac_seq_Lerchter_3153_160217A3-se-1.json → ...atac_seq_Lerchter_3153_160217A3-se-1.json
diff --git a/...3153_160217A3-se-blacklist-removal-0.json → ...3153_160217A3-se-blacklist-removal-0.json b/...3153_160217A3-se-blacklist-removal-0.json → ...3153_160217A3-se-blacklist-removal-0.json
diff --git a/...3153_160217A3-se-blacklist-removal-1.json → ...3153_160217A3-se-blacklist-removal-1.json b/...3153_160217A3-se-blacklist-removal-1.json → ...3153_160217A3-se-blacklist-removal-1.json
diff --git a/...r_3153_160217A3-se-blacklist-removal.json → ...r_3153_160217A3-se-blacklist-removal.json b/...r_3153_160217A3-se-blacklist-removal.json → ...r_3153_160217A3-se-blacklist-removal.json
diff --git a/...q/atac_seq_Lerchter_3153_160217A3-se.json → ...q/atac_seq_Lerchter_3153_160217A3-se.json b/...q/atac_seq_Lerchter_3153_160217A3-se.json → ...q/atac_seq_Lerchter_3153_160217A3-se.json
diff --git a/...c_seq/atac_seq_Lerchter_3153_160217A3.txt → ...c_seq/atac_seq_Lerchter_3153_160217A3.txt b/...c_seq/atac_seq_Lerchter_3153_160217A3.txt → ...c_seq/atac_seq_Lerchter_3153_160217A3.txt
diff --git a/..._3153_160217A3-se-broad-with-control.json → ..._3153_160217A3-se-broad-with-control.json b/..._3153_160217A3-se-broad-with-control.json → ..._3153_160217A3-se-broad-with-control.json
diff --git a/...3153_160217A3-se-narrow-with-control.json → ...3153_160217A3-se-narrow-with-control.json b/...3153_160217A3-se-narrow-with-control.json → ...3153_160217A3-se-narrow-with-control.json
diff --git a/...p_seq/chip_seq_Lerchter_3153_160217A3.txt → ...p_seq/chip_seq_Lerchter_3153_160217A3.txt b/...p_seq/chip_seq_Lerchter_3153_160217A3.txt → ...p_seq/chip_seq_Lerchter_3153_160217A3.txt
diff --git a/...ownload_metadata.ALL.iter-1-pe-broad.json → ...ownload_metadata.ALL.iter-1-pe-broad.json b/...ownload_metadata.ALL.iter-1-pe-broad.json → ...ownload_metadata.ALL.iter-1-pe-broad.json
diff --git a/...wnload_metadata.ALL.iter-1-pe-narrow.json → ...wnload_metadata.ALL.iter-1-pe-narrow.json b/...wnload_metadata.ALL.iter-1-pe-narrow.json → ...wnload_metadata.ALL.iter-1-pe-narrow.json
diff --git a/...ownload_metadata.ALL.iter-1-se-broad.json → ...ownload_metadata.ALL.iter-1-se-broad.json b/...ownload_metadata.ALL.iter-1-se-broad.json → ...ownload_metadata.ALL.iter-1-se-broad.json
diff --git a/...wnload_metadata.ALL.iter-1-se-narrow.json → ...wnload_metadata.ALL.iter-1-se-narrow.json b/...wnload_metadata.ALL.iter-1-se-narrow.json → ...wnload_metadata.ALL.iter-1-se-narrow.json
diff --git a/...chip_seq_download_metadata.ALL.iter-1.txt → ...chip_seq_download_metadata.ALL.iter-1.txt b/...chip_seq_download_metadata.ALL.iter-1.txt → ...chip_seq_download_metadata.ALL.iter-1.txt
diff --git a/...tadata.Project_Hong_2574_150702A3-pe.json → ...tadata.Project_Hong_2574_150702A3-pe.json b/...tadata.Project_Hong_2574_150702A3-pe.json → ...tadata.Project_Hong_2574_150702A3-pe.json
diff --git a/...d_metadata.Project_Hong_2574_150702A3.txt → ...d_metadata.Project_Hong_2574_150702A3.txt b/...d_metadata.Project_Hong_2574_150702A3.txt → ...d_metadata.Project_Hong_2574_150702A3.txt
diff --git a/json-generator/run.py → draft-3/json-generator/run.py b/json-generator/run.py → draft-3/json-generator/run.py
diff --git a/json-generator/templates/atac-seq.j2 → draft-3/json-generator/templates/atac-seq.j2 b/json-generator/templates/atac-seq.j2 → draft-3/json-generator/templates/atac-seq.j2
diff --git a/json-generator/templates/chip-seq.j2 → draft-3/json-generator/templates/chip-seq.j2 b/json-generator/templates/chip-seq.j2 → draft-3/json-generator/templates/chip-seq.j2
diff --git a/json-generator/templates/rna-seq.j2 → draft-3/json-generator/templates/rna-seq.j2 b/json-generator/templates/rna-seq.j2 → draft-3/json-generator/templates/rna-seq.j2
diff --git a/map/bedtools-bamtobed.cwl → draft-3/map/bedtools-bamtobed.cwl b/map/bedtools-bamtobed.cwl → draft-3/map/bedtools-bamtobed.cwl
diff --git a/map/bedtools-bedtobam.cwl → draft-3/map/bedtools-bedtobam.cwl b/map/bedtools-bedtobam.cwl → draft-3/map/bedtools-bedtobam.cwl
diff --git a/map/bedtools-genomecov.cwl → draft-3/map/bedtools-genomecov.cwl b/map/bedtools-genomecov.cwl → draft-3/map/bedtools-genomecov.cwl
diff --git a/map/bedtools-intersect.cwl → draft-3/map/bedtools-intersect.cwl b/map/bedtools-intersect.cwl → draft-3/map/bedtools-intersect.cwl
diff --git a/map/bowtie-log-read-count.cwl → draft-3/map/bowtie-log-read-count.cwl b/map/bowtie-log-read-count.cwl → draft-3/map/bowtie-log-read-count.cwl
diff --git a/map/bowtie-pe.cwl → draft-3/map/bowtie-pe.cwl b/map/bowtie-pe.cwl → draft-3/map/bowtie-pe.cwl
diff --git a/map/bowtie-se.cwl → draft-3/map/bowtie-se.cwl b/map/bowtie-se.cwl → draft-3/map/bowtie-se.cwl
diff --git a/map/compute-pbc.cwl → draft-3/map/compute-pbc.cwl b/map/compute-pbc.cwl → draft-3/map/compute-pbc.cwl
diff --git a/map/create-conservative-sjdb.cwl → draft-3/map/create-conservative-sjdb.cwl b/map/create-conservative-sjdb.cwl → draft-3/map/create-conservative-sjdb.cwl
diff --git a/map/filter-pcr-artifacts.cwl → draft-3/map/filter-pcr-artifacts.cwl b/map/filter-pcr-artifacts.cwl → draft-3/map/filter-pcr-artifacts.cwl
diff --git a/map/pcr-bottleneck-coef.cwl → draft-3/map/pcr-bottleneck-coef.cwl b/map/pcr-bottleneck-coef.cwl → draft-3/map/pcr-bottleneck-coef.cwl
diff --git a/map/picard-MarkDuplicates.cwl → draft-3/map/picard-MarkDuplicates.cwl b/map/picard-MarkDuplicates.cwl → draft-3/map/picard-MarkDuplicates.cwl
diff --git a/map/preseq-c_curve.cwl → draft-3/map/preseq-c_curve.cwl b/map/preseq-c_curve.cwl → draft-3/map/preseq-c_curve.cwl
diff --git a/map/preseq-lc_extrap.cwl → draft-3/map/preseq-lc_extrap.cwl b/map/preseq-lc_extrap.cwl → draft-3/map/preseq-lc_extrap.cwl
diff --git a/map/preseq-percent-uniq-reads.cwl → draft-3/map/preseq-percent-uniq-reads.cwl b/map/preseq-percent-uniq-reads.cwl → draft-3/map/preseq-percent-uniq-reads.cwl
diff --git a/map/samtools-filter-unmapped.cwl → draft-3/map/samtools-filter-unmapped.cwl b/map/samtools-filter-unmapped.cwl → draft-3/map/samtools-filter-unmapped.cwl
diff --git a/map/samtools-index.cwl → draft-3/map/samtools-index.cwl b/map/samtools-index.cwl → draft-3/map/samtools-index.cwl
diff --git a/map/samtools-sort.cwl → draft-3/map/samtools-sort.cwl b/map/samtools-sort.cwl → draft-3/map/samtools-sort.cwl
diff --git a/map/samtools-view-sam.cwl → draft-3/map/samtools-view-sam.cwl b/map/samtools-view-sam.cwl → draft-3/map/samtools-view-sam.cwl
diff --git a/map/samtools2bam.cwl → draft-3/map/samtools2bam.cwl b/map/samtools2bam.cwl → draft-3/map/samtools2bam.cwl
diff --git a/map/star-log-read-count.cwl → draft-3/map/star-log-read-count.cwl b/map/star-log-read-count.cwl → draft-3/map/star-log-read-count.cwl
diff --git a/map/windowtrimmer.cwl → draft-3/map/windowtrimmer.cwl b/map/windowtrimmer.cwl → draft-3/map/windowtrimmer.cwl
diff --git a/peak_calling/bedpe-to-bed.cwl → draft-3/peak_calling/bedpe-to-bed.cwl b/peak_calling/bedpe-to-bed.cwl → draft-3/peak_calling/bedpe-to-bed.cwl
diff --git a/peak_calling/count-reads-after-filtering.cwl → ...k_calling/count-reads-after-filtering.cwl b/peak_calling/count-reads-after-filtering.cwl → ...k_calling/count-reads-after-filtering.cwl
diff --git a/peak_calling/macs2-callpeak.cwl → draft-3/peak_calling/macs2-callpeak.cwl b/peak_calling/macs2-callpeak.cwl → draft-3/peak_calling/macs2-callpeak.cwl
diff --git a/.../samtools-extract-number-mapped-reads.cwl → .../samtools-extract-number-mapped-reads.cwl b/.../samtools-extract-number-mapped-reads.cwl → .../samtools-extract-number-mapped-reads.cwl
diff --git a/peak_calling/samtools-filter-in-bedfile.cwl → ...ak_calling/samtools-filter-in-bedfile.cwl b/peak_calling/samtools-filter-in-bedfile.cwl → ...ak_calling/samtools-filter-in-bedfile.cwl
diff --git a/peak_calling/scale-bedgraph.cwl → draft-3/peak_calling/scale-bedgraph.cwl b/peak_calling/scale-bedgraph.cwl → draft-3/peak_calling/scale-bedgraph.cwl
diff --git a/qc/count-fastqc-reads.cwl → draft-3/qc/count-fastqc-reads.cwl b/qc/count-fastqc-reads.cwl → draft-3/qc/count-fastqc-reads.cwl
diff --git a/qc/diff.cwl → draft-3/qc/diff.cwl b/qc/diff.cwl → draft-3/qc/diff.cwl
diff --git a/qc/extract_fastqc_data.cwl → draft-3/qc/extract_fastqc_data.cwl b/qc/extract_fastqc_data.cwl → draft-3/qc/extract_fastqc_data.cwl
diff --git a/qc/fastqc.cwl → draft-3/qc/fastqc.cwl b/qc/fastqc.cwl → draft-3/qc/fastqc.cwl
diff --git a/qc/overrepresented_sequence_extract.cwl → ...3/qc/overrepresented_sequence_extract.cwl b/qc/overrepresented_sequence_extract.cwl → ...3/qc/overrepresented_sequence_extract.cwl
diff --git a/quant/bamtools-filter.cwl → draft-3/quant/bamtools-filter.cwl b/quant/bamtools-filter.cwl → draft-3/quant/bamtools-filter.cwl
diff --git a/quant/bedClip.cwl → draft-3/quant/bedClip.cwl b/quant/bedClip.cwl → draft-3/quant/bedClip.cwl
diff --git a/quant/bedGraphToBigWig.cwl → draft-3/quant/bedGraphToBigWig.cwl b/quant/bedGraphToBigWig.cwl → draft-3/quant/bedGraphToBigWig.cwl
diff --git a/quant/bedSort.cwl → draft-3/quant/bedSort.cwl b/quant/bedSort.cwl → draft-3/quant/bedSort.cwl
diff --git a/quant/bedToBigBed.cwl → draft-3/quant/bedToBigBed.cwl b/quant/bedToBigBed.cwl → draft-3/quant/bedToBigBed.cwl
diff --git a/quant/bedtools-slop.cwl → draft-3/quant/bedtools-slop.cwl b/quant/bedtools-slop.cwl → draft-3/quant/bedtools-slop.cwl
diff --git a/quant/bigWigToBedGraph.cwl → draft-3/quant/bigWigToBedGraph.cwl b/quant/bigWigToBedGraph.cwl → draft-3/quant/bigWigToBedGraph.cwl
diff --git a/quant/convert-sam-for-rsem.cwl → draft-3/quant/convert-sam-for-rsem.cwl b/quant/convert-sam-for-rsem.cwl → draft-3/quant/convert-sam-for-rsem.cwl
diff --git a/quant/deeptools-bamcoverage.cwl → draft-3/quant/deeptools-bamcoverage.cwl b/quant/deeptools-bamcoverage.cwl → draft-3/quant/deeptools-bamcoverage.cwl
diff --git a/quant/deeptools-bigwigcompare.cwl → draft-3/quant/deeptools-bigwigcompare.cwl b/quant/deeptools-bigwigcompare.cwl → draft-3/quant/deeptools-bigwigcompare.cwl
diff --git a/quant/deeptools-multiBigwigSummary-bins.cwl → ...ant/deeptools-multiBigwigSummary-bins.cwl b/quant/deeptools-multiBigwigSummary-bins.cwl → ...ant/deeptools-multiBigwigSummary-bins.cwl
diff --git a/quant/negate-minus-strand-bedgraph.cwl → ...-3/quant/negate-minus-strand-bedgraph.cwl b/quant/negate-minus-strand-bedgraph.cwl → ...-3/quant/negate-minus-strand-bedgraph.cwl
diff --git a/quant/rsem-calculate-expression.cwl → draft-3/quant/rsem-calculate-expression.cwl b/quant/rsem-calculate-expression.cwl → draft-3/quant/rsem-calculate-expression.cwl
diff --git a/quant/rsem-prepare-reference.cwl → draft-3/quant/rsem-prepare-reference.cwl b/quant/rsem-prepare-reference.cwl → draft-3/quant/rsem-prepare-reference.cwl
diff --git a/quant/split-bams-by-strand-and-index.cwl → .../quant/split-bams-by-strand-and-index.cwl b/quant/split-bams-by-strand-and-index.cwl → .../quant/split-bams-by-strand-and-index.cwl
diff --git a/quant/subread-featurecounts.cwl → draft-3/quant/subread-featurecounts.cwl b/quant/subread-featurecounts.cwl → draft-3/quant/subread-featurecounts.cwl
diff --git a/...atac-seq/03-map-pe-blacklist-removal.json → ...atac-seq/03-map-pe-blacklist-removal.json b/...atac-seq/03-map-pe-blacklist-removal.json → ...atac-seq/03-map-pe-blacklist-removal.json
diff --git a/scripts_local_run/atac-seq/03-map-pe.json → ...scripts_local_run/atac-seq/03-map-pe.json b/scripts_local_run/atac-seq/03-map-pe.json → ...scripts_local_run/atac-seq/03-map-pe.json
diff --git a/...ocal_run/atac-seq/pipeline-pe-narrow.json → ...ocal_run/atac-seq/pipeline-pe-narrow.json b/...ocal_run/atac-seq/pipeline-pe-narrow.json → ...ocal_run/atac-seq/pipeline-pe-narrow.json
diff --git a/...ocal_run/atac-seq/pipeline-se-narrow.json → ...ocal_run/atac-seq/pipeline-se-narrow.json b/...ocal_run/atac-seq/pipeline-se-narrow.json → ...ocal_run/atac-seq/pipeline-se-narrow.json
diff --git a/scripts_local_run/chip-seq/01-qc-se.json → .../scripts_local_run/chip-seq/01-qc-se.json b/scripts_local_run/chip-seq/01-qc-se.json → .../scripts_local_run/chip-seq/01-qc-se.json
diff --git a/scripts_local_run/chip-seq/02-trim-pe.json → ...cripts_local_run/chip-seq/02-trim-pe.json b/scripts_local_run/chip-seq/02-trim-pe.json → ...cripts_local_run/chip-seq/02-trim-pe.json
diff --git a/scripts_local_run/chip-seq/02-trim-se.json → ...cripts_local_run/chip-seq/02-trim-se.json b/scripts_local_run/chip-seq/02-trim-se.json → ...cripts_local_run/chip-seq/02-trim-se.json
diff --git a/scripts_local_run/chip-seq/03-map-se.json → ...scripts_local_run/chip-seq/03-map-se.json b/scripts_local_run/chip-seq/03-map-se.json → ...scripts_local_run/chip-seq/03-map-se.json
diff --git a/...-seq/04-peakcall-narrow-with-control.json → ...-seq/04-peakcall-narrow-with-control.json b/...-seq/04-peakcall-narrow-with-control.json → ...-seq/04-peakcall-narrow-with-control.json
diff --git a/...ocal_run/chip-seq/04-peakcall-narrow.json → ...ocal_run/chip-seq/04-peakcall-narrow.json b/...ocal_run/chip-seq/04-peakcall-narrow.json → ...ocal_run/chip-seq/04-peakcall-narrow.json
diff --git a/...local_run/chip-seq/05-quantification.json → ...local_run/chip-seq/05-quantification.json b/...local_run/chip-seq/05-quantification.json → ...local_run/chip-seq/05-quantification.json
diff --git a/...ocal_run/chip-seq/pipeline-pe-narrow.json → ...ocal_run/chip-seq/pipeline-pe-narrow.json b/...ocal_run/chip-seq/pipeline-pe-narrow.json → ...ocal_run/chip-seq/pipeline-pe-narrow.json
diff --git a/...-seq/pipeline-se-narrow-with-control.json → ...-seq/pipeline-se-narrow-with-control.json b/...-seq/pipeline-se-narrow-with-control.json → ...-seq/pipeline-se-narrow-with-control.json
diff --git a/...ocal_run/chip-seq/pipeline-se-narrow.json → ...ocal_run/chip-seq/pipeline-se-narrow.json b/...ocal_run/chip-seq/pipeline-se-narrow.json → ...ocal_run/chip-seq/pipeline-se-narrow.json
diff --git a/..._run/chip-seq/run_bowtie-se_tool_local.sh → ..._run/chip-seq/run_bowtie-se_tool_local.sh b/..._run/chip-seq/run_bowtie-se_tool_local.sh → ..._run/chip-seq/run_bowtie-se_tool_local.sh
diff --git a/scripts_local_run/chip-seq/run_local.sh → ...3/scripts_local_run/chip-seq/run_local.sh b/scripts_local_run/chip-seq/run_local.sh → ...3/scripts_local_run/chip-seq/run_local.sh
diff --git a/...pts_local_run/chip-seq/run_qc-pe_local.sh → ...pts_local_run/chip-seq/run_qc-pe_local.sh b/...pts_local_run/chip-seq/run_qc-pe_local.sh → ...pts_local_run/chip-seq/run_qc-pe_local.sh
diff --git a/scripts_local_run/chip-seq/run_qc_local.sh → ...cripts_local_run/chip-seq/run_qc_local.sh b/scripts_local_run/chip-seq/run_qc_local.sh → ...cripts_local_run/chip-seq/run_qc_local.sh
diff --git a/..._run/chip-seq/run_trimmomatic-pe_local.sh → ..._run/chip-seq/run_trimmomatic-pe_local.sh b/..._run/chip-seq/run_trimmomatic-pe_local.sh → ..._run/chip-seq/run_trimmomatic-pe_local.sh
diff --git a/...chip-seq/run_trimmomatic-pe_tool_local.sh → ...chip-seq/run_trimmomatic-pe_tool_local.sh b/...chip-seq/run_trimmomatic-pe_tool_local.sh → ...chip-seq/run_trimmomatic-pe_tool_local.sh
diff --git a/..._run/chip-seq/run_trimmomatic-se_local.sh → ..._run/chip-seq/run_trimmomatic-se_local.sh b/..._run/chip-seq/run_trimmomatic-se_local.sh → ..._run/chip-seq/run_trimmomatic-se_local.sh
diff --git a/...chip-seq/run_trimmomatic-se_tool_local.sh → ...chip-seq/run_trimmomatic-se_tool_local.sh b/...chip-seq/run_trimmomatic-se_tool_local.sh → ...chip-seq/run_trimmomatic-se_tool_local.sh
diff --git a/scripts_local_run/dnase-seq/01-map-se.json → ...cripts_local_run/dnase-seq/01-map-se.json b/scripts_local_run/dnase-seq/01-map-se.json → ...cripts_local_run/dnase-seq/01-map-se.json
diff --git a/scripts_local_run/dnase-seq/02-peakcall.json → ...ipts_local_run/dnase-seq/02-peakcall.json b/scripts_local_run/dnase-seq/02-peakcall.json → ...ipts_local_run/dnase-seq/02-peakcall.json
diff --git a/...ocal_run/dnase-seq/03-quantification.json → ...ocal_run/dnase-seq/03-quantification.json b/...ocal_run/dnase-seq/03-quantification.json → ...ocal_run/dnase-seq/03-quantification.json
diff --git a/scripts_local_run/dnase-seq/pipeline-se.json → ...ipts_local_run/dnase-seq/pipeline-se.json b/scripts_local_run/dnase-seq/pipeline-se.json → ...ipts_local_run/dnase-seq/pipeline-se.json
diff --git a/...s_local_run/rna-seq/00-preprocessing.json → ...s_local_run/rna-seq/00-preprocessing.json b/...s_local_run/rna-seq/00-preprocessing.json → ...s_local_run/rna-seq/00-preprocessing.json
diff --git a/scripts_local_run/rna-seq/01-qc-se.json → ...3/scripts_local_run/rna-seq/01-qc-se.json b/scripts_local_run/rna-seq/01-qc-se.json → ...3/scripts_local_run/rna-seq/01-qc-se.json
diff --git a/...s_local_run/rna-seq/03-map-pe-nostar.json → ...s_local_run/rna-seq/03-map-pe-nostar.json b/...s_local_run/rna-seq/03-map-pe-nostar.json → ...s_local_run/rna-seq/03-map-pe-nostar.json
diff --git a/scripts_local_run/rna-seq/03-map-pe.json → .../scripts_local_run/rna-seq/03-map-pe.json b/scripts_local_run/rna-seq/03-map-pe.json → .../scripts_local_run/rna-seq/03-map-pe.json
diff --git a/..._local_run/rna-seq/04-quantification.json → ...cal_run/rna-seq/04-quantification-se.json b/..._local_run/rna-seq/04-quantification.json → ...cal_run/rna-seq/04-quantification-se.json
diff --git a/...al_run/rna-seq/pipeline-pe-with-sjdb.json → ...al_run/rna-seq/pipeline-pe-with-sjdb.json b/...al_run/rna-seq/pipeline-pe-with-sjdb.json → ...al_run/rna-seq/pipeline-pe-with-sjdb.json
diff --git a/scripts_local_run/rna-seq/pipeline-pe.json → ...cripts_local_run/rna-seq/pipeline-pe.json b/scripts_local_run/rna-seq/pipeline-pe.json → ...cripts_local_run/rna-seq/pipeline-pe.json
diff --git a/scripts_local_run/rna-seq/pipeline-se.json → ...cripts_local_run/rna-seq/pipeline-se.json b/scripts_local_run/rna-seq/pipeline-se.json → ...cripts_local_run/rna-seq/pipeline-se.json
diff --git a/...seq/rsem-1.2.21-calculate-expression.json → ...seq/rsem-1.2.21-calculate-expression.json b/...seq/rsem-1.2.21-calculate-expression.json → ...seq/rsem-1.2.21-calculate-expression.json
diff --git a/...un/rna-seq/rsem-calculate-expression.json → ...un/rna-seq/rsem-calculate-expression.json b/...un/rna-seq/rsem-calculate-expression.json → ...un/rna-seq/rsem-calculate-expression.json
diff --git a/scripts_slurm_run/03-map-pe.json → draft-3/scripts_slurm_run/03-map-pe.json b/scripts_slurm_run/03-map-pe.json → draft-3/scripts_slurm_run/03-map-pe.json
diff --git a/scripts_slurm_run/atac-seq/03-map-pe.json → ...scripts_slurm_run/atac-seq/03-map-pe.json b/scripts_slurm_run/atac-seq/03-map-pe.json → ...scripts_slurm_run/atac-seq/03-map-pe.json
diff --git a/scripts_slurm_run/run_qc_hardac.sh → draft-3/scripts_slurm_run/run_qc_hardac.sh b/scripts_slurm_run/run_qc_hardac.sh → draft-3/scripts_slurm_run/run_qc_hardac.sh
diff --git a/spp/extract-best-frag-length.cwl → draft-3/spp/extract-best-frag-length.cwl b/spp/extract-best-frag-length.cwl → draft-3/spp/extract-best-frag-length.cwl
diff --git a/spp/spp.cwl → draft-3/spp/spp.cwl b/spp/spp.cwl → draft-3/spp/spp.cwl
diff --git a/trimmomatic/trimmomatic.cwl → draft-3/trimmomatic/trimmomatic.cwl b/trimmomatic/trimmomatic.cwl → draft-3/trimmomatic/trimmomatic.cwl
@@ -48,7 +48,7 @@ inputs:
         <keepBothReads>: After read-though has been detected by palindrome mode, and the
         adapter sequence removed, the reverse read contains the same sequence information as the
         forward read, albeit in reverse complement. For this reason, the default behaviour is to
-        entirely drop the reverse read. By specifying „true‟ for this parameter, the reverse read will
+        entirely drop the reverse read. By specifying "true" for this parameter, the reverse read will
         also be retained, which may be useful e.g. if the downstream tools cannot handle a
         combination of paired and unpaired reads.
   - id: slidingwindow
@@ -100,9 +100,9 @@ inputs:
     description: |
       <quality>
       Remove low quality bases from the end. As long as a base has a value below this threshold
-      the base is removed and the next base (which as trimmomatic is starting from the 3‟ prime end
+      the base is removed and the next base (which as trimmomatic is starting from the 3" prime end
       would be base preceding the just removed base) will be investigated. This approach can be
-      used removing the special illumina „low quality segment‟ regions (which are marked with
+      used removing the special illumina "low quality segment" regions (which are marked with
       quality score of 2), but we recommend Sliding Window or MaxInfo instead
       <quality>: Specifies the minimum quality required to keep a base.
   - id: crop
@@ -137,7 +137,7 @@ inputs:
       <length>
       This module removes reads that fall below the specified minimal length. If required, it should
       normally be after all other processing steps. Reads removed by this step will be counted and
-      included in the „dropped reads‟ count presented in the trimmomatic summary.
+      included in the "dropped reads" count presented in the trimmomatic summary.
       <length>:  Specifies the minimum length of reads to be kept
   - id: avgqual
     type: ['null', int]

diff --git a/utils/basename.cwl → draft-3/utils/basename.cwl b/utils/basename.cwl → draft-3/utils/basename.cwl
diff --git a/utils/concat-files.cwl → draft-3/utils/concat-files.cwl b/utils/concat-files.cwl → draft-3/utils/concat-files.cwl
diff --git a/utils/count-fastq-reads.cwl → draft-3/utils/count-fastq-reads.cwl b/utils/count-fastq-reads.cwl → draft-3/utils/count-fastq-reads.cwl
diff --git a/utils/count-with-output-suffix.cwl → draft-3/utils/count-with-output-suffix.cwl b/utils/count-with-output-suffix.cwl → draft-3/utils/count-with-output-suffix.cwl
diff --git a/utils/extract-basename.cwl → draft-3/utils/extract-basename.cwl b/utils/extract-basename.cwl → draft-3/utils/extract-basename.cwl
diff --git a/utils/remove-extension.cwl → draft-3/utils/remove-extension.cwl b/utils/remove-extension.cwl → draft-3/utils/remove-extension.cwl
diff --git a/utils/split_file_with_secondaryFiles.cwl → .../utils/split_file_with_secondaryFiles.cwl b/utils/split_file_with_secondaryFiles.cwl → .../utils/split_file_with_secondaryFiles.cwl
diff --git a/utils/trunk-peak-score.cwl → draft-3/utils/trunk-peak-score.cwl b/utils/trunk-peak-score.cwl → draft-3/utils/trunk-peak-score.cwl
diff --git a/utils/zip_arrays.cwl → draft-3/utils/zip_arrays.cwl b/utils/zip_arrays.cwl → draft-3/utils/zip_arrays.cwl