Refactor the whole file structure for future pipelines (#139)

* Refactor the modules and files accoording to the discussion, fixed the imports, test would fail though.

* Refactor the testing modules and files accoording to the discussion, fixed the imports, test should pass.

* Update the package structures and CLI to adapt to the adapters.

* Update the adapter WDLS.

Author: rexwangcc

adapter_pipelines/Optimus/adapter.wdl

@@ -22,12 +22,12 @@ task GetInputs {
 
     # Force the binary layer of the stdout and stderr streams to be unbuffered.
     python -u <<CODE
-    from pipeline_tools import input_utils
+    from pipeline_tools.pipelines.optimus import optimus
 
-    input_utils.create_optimus_input_tsv(
-                    "${bundle_uuid}",
-                    "${bundle_version}",
-                    "${dss_url}")
+    optimus.create_optimus_input_tsv(
+                "${bundle_uuid}",
+                "${bundle_version}",
+                "${dss_url}")
 
     CODE
   >>>
@@ -139,7 +139,7 @@ workflow AdapterOptimus {
   Int max_cromwell_retries = 0
   Boolean add_md5s = false
 
-  String pipeline_tools_version = "v0.49.1"
+  String pipeline_tools_version = "v0.50.0"
 
   call GetInputs as prep {
     input:

adapter_pipelines/cellranger/adapter.wdl

@@ -22,12 +22,12 @@ task GetInputs {
 
     # Force the binary layer of the stdout and stderr streams to be unbuffered.
     python -u <<CODE
-    from pipeline_tools import input_utils
+    from pipeline_tools.pipelines.cellranger import cellranger
 
-    input_utils.get_cellranger_input_files(
-                    "${bundle_uuid}",
-                    "${bundle_version}",
-                    "${dss_url}")
+    cellranger.create_cellranger_input_tsv(
+                  "${bundle_uuid}",
+                  "${bundle_version}",
+                  "${dss_url}")
 
     CODE
   >>>
@@ -150,7 +150,7 @@ workflow Adapter10xCount {
   Int max_cromwell_retries = 0
   Boolean add_md5s = false
 
-  String pipeline_tools_version = "v0.49.1"
+  String pipeline_tools_version = "v0.50.0"
 
   call GetInputs {
     input:

adapter_pipelines/ss2_single_sample/adapter.wdl

@@ -22,12 +22,12 @@ task GetInputs {
 
     # Force the binary layer of the stdout and stderr streams to be unbuffered.
     python -u <<CODE
-    from pipeline_tools import input_utils
+    from pipeline_tools.pipelines.smartseq2 import smartseq2
 
-    input_utils.create_ss2_input_tsv(
-                    "${bundle_uuid}",
-                    "${bundle_version}",
-                    "${dss_url}")
+    smartseq2.create_ss2_input_tsv(
+                  "${bundle_uuid}",
+                  "${bundle_version}",
+                  "${dss_url}")
 
     CODE
   >>>
@@ -82,7 +82,7 @@ workflow AdapterSmartSeq2SingleCell{
   Int max_cromwell_retries = 0
   Boolean add_md5s = false
 
-  String pipeline_tools_version = "v0.49.1"
+  String pipeline_tools_version = "v0.50.0"
 
   call GetInputs as prep {
     input: