Merge pull request #140 from NAL-i5K/annotation-symlink

Add functional annotation directory symlink

CreateSymlink-workflow.cwl

@@ -116,17 +116,30 @@ steps:
       deepPATH_analyses: deepPATH_analyses
       MAIN_PATH: MAIN_PATH
     out: [out_dummy]
-  #step6 gzip - bigwig files
+  #step6 symlink - functional annotation folder
+  annotation_symlink:
+    run: flow_reorganize_symlinks/annotation_symlink.cwl
+    when: $(inputs.tree[3] != "NA")
+    in:
+      in_dummy: analyses_symlink/out_dummy
+      PATH: PATH
+      tree: tree
+      scientific_name: scientific_name
+      deepPATH_genomic_fasta: deepPATH_genomic_fasta
+      deepPATH_analyses: deepPATH_analyses
+      MAIN_PATH: MAIN_PATH
+    out: [out_dummy]
+  #step7 gzip - bigwig files
   bigwig_gzip:
     run: flow_reorganize_symlinks/bigwig_gzip.cwl
     in:
-      in_dummy: analyses_symlink/out_dummy
+      in_dummy: annotation_symlink/out_dummy
       PATH: PATH
       tree: tree
       genome_fasta_name: genome_fasta_name
       deepPATH_bigwig: deepPATH_bigwig
     out: [out_dummy]
-  #step7 symlink - bigwig files-gaps
+  #step8 symlink - bigwig files-gaps
   bigwig_symlink-gaps:
     run: flow_reorganize_symlinks/bigwig_symlink-gaps.cwl 
     in:
@@ -138,7 +151,7 @@ steps:
       deepPATH_bigwig: deepPATH_bigwig
       MAIN_PATH: MAIN_PATH
     out: [out_dummy]
-  #step8 symlink - bigwig files-gc
+  #step9 symlink - bigwig files-gc
   bigwig_symlink-gc:
     run: flow_reorganize_symlinks/bigwig_symlink-gc.cwl
     in:
@@ -150,7 +163,7 @@ steps:
       deepPATH_bigwig: deepPATH_bigwig
       MAIN_PATH: MAIN_PATH
     out: [out_dummy]
-  #step9 symlink - assembly folder
+  #step10 symlink - assembly folder
   assembly_symlink:
     run: flow_reorganize_symlinks/assembly_symlink.cwl
     in:

final-workflow-short.yml

@@ -32,7 +32,8 @@ hmmerdb_Path_production: [/usr/local/i5k/media/hmmer/db]
 tree: [
 saceub, #species abbreviation - format gggsss
 SEUB3.0, #the assembly name
-Saccharomyces_eubayanus_Annotation_Release_100 #the gene set/annotation name
+Saccharomyces_eubayanus_Annotation_Release_100, #the gene set/annotation name
+NA #the functional annotation directory name, which should be in the analyses/ folder. Add 'NA' if not applicable.
 ]
 scientific_name: [
 Saccharomyces, #genus

final-workflow.yml

@@ -32,7 +32,8 @@ hmmerdb_Path_production: [/usr/local/i5k/media/hmmer/db]
 tree: [
 apimel, #species abbreviation - format gggsss
 Amel_HAv3.1, #the assembly name
-Apis_mellifera_Annotation_Release_103 #the gene set/annotation name
+Apis_mellifera_Annotation_Release_103, #the gene set/annotation name
+NA #the functional annotation directory name, which should be in the analyses/ folder. Add 'NA' if not applicable.
 ]
 scientific_name: [
 Apis, #genus

flow_reorganize_symlinks/annotation_symlink.cwl

@@ -0,0 +1,38 @@
+#!usr/bin/env cwl-runner
+
+cwlVersion: v1.2
+class: CommandLineTool
+
+requirements:
+  - class: InlineJavascriptRequirement
+
+baseCommand: [ln]
+arguments:
+  - prefix: -s
+    #functional annotation directory
+    position: 1
+    valueFrom: $(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_genomic_fasta[0])/$(inputs.deepPATH_analyses[0])/$(inputs.tree[3])
+    #target directory
+  - position: 2
+    valueFrom: $(inputs.MAIN_PATH)/$(inputs.tree[0])-($(inputs.scientific_name[0])_$(inputs.scientific_name[1]))/$(inputs.tree[1])/2.Official or Primary Gene Set/.
+
+inputs:
+  in_dummy: 
+    type: File
+  PATH:
+    type: string[]
+  tree:
+    type: string[]
+  scientific_name: 
+    type: string[]
+  deepPATH_genomic_fasta:
+    type: string[]
+  deepPATH_analyses:
+    type: string[]
+  MAIN_PATH:
+    type: string
+
+outputs:
+  out_dummy:
+    type: stdout
+stdout: annotation_symlink.dummy

flow_reorganize_symlinks/bigwig_gzip.cwl

@@ -17,7 +17,7 @@ arguments:
 
 inputs:
   in_dummy: 
-    type: File
+    type: File?
   PATH:
     type: string[]
   tree: