add mercury workflows

theiagen · Feb 23, 2021 · ddbc83b · ddbc83b
1 parent 841b5c3
commit ddbc83b
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Showing 6 changed files with 22 additions and 7 deletions.
diff --git a/.dockstore.yml b/.dockstore.yml
@@ -55,3 +55,18 @@ workflows:
    primaryDescriptorPath: /workflows/wf_sc2_pubRepo_prep_pe.wdl
    testParameterFiles:
     - empty.json
+ - name: Mercury_PE_Prep
+   subclass: WDL
+   primaryDescriptorPath: /workflows/wf_mercury_pe_prep.wdl
+   testParameterFiles:
+    - empty.json
+ - name: Mercury_SE_Prep
+   subclass: WDL
+   primaryDescriptorPath: /workflows/wf_mercury_se_prep.wdl
+   testParameterFiles:
+    - empty.json
+ - name: Mercury_Batch
+   subclass: WDL
+   primaryDescriptorPath: /workflows/wf_mercury_batch.wdl
+   testParameterFiles:
+    - empty.json
diff --git a/tasks/task_pub_repo_submission.wdl → tasks/task_pe_pub_repo_submission.wdl b/tasks/task_pub_repo_submission.wdl → tasks/task_pe_pub_repo_submission.wdl
diff --git a/tasks/task_ont_pub_repo_submission.wdl → tasks/task_se_pub_repo_submission.wdl b/tasks/task_ont_pub_repo_submission.wdl → tasks/task_se_pub_repo_submission.wdl
diff --git a/workflows/wf_sc2_batch_submission.wdl → workflows/wf_mercury_batch.wdl b/workflows/wf_sc2_batch_submission.wdl → workflows/wf_mercury_batch.wdl
@@ -1,8 +1,8 @@
 version 1.0
 
-import "../tasks/task_ont_pub_repo_submission.wdl" as submission
+import "../tasks/task_se_pub_repo_submission.wdl" as submission
 
-workflow batch_fasta_repo_submission {
+workflow mercury_batch {
 	input {
 		Array[File] genbank_single_submission_fasta
 		Array[File] genbank_single_submission_meta

diff --git a/workflows/wf_sc2_pubRepo_prep_pe.wdl → workflows/wf_mercury_pe_prep.wdl b/workflows/wf_sc2_pubRepo_prep_pe.wdl → workflows/wf_mercury_pe_prep.wdl
@@ -1,8 +1,8 @@
 version 1.0
 
-import "../tasks/task_pub_repo_submission.wdl" as submission
+import "../tasks/task_pe_pub_repo_submission.wdl" as submission
 
-workflow SC2_submission_files {
+workflow mercury_pe_prep {
 	input {
 		String 		samplename
 		String		submission_id

diff --git a/workflows/wf_sc2_pubRepo_prep_se.wdl → workflows/wf_mercury_se_prep.wdl b/workflows/wf_sc2_pubRepo_prep_se.wdl → workflows/wf_mercury_se_prep.wdl
@@ -1,8 +1,8 @@
 version 1.0
 
-import "../tasks/task_ont_pub_repo_submission.wdl" as submission
+import "../tasks/task_se_pub_repo_submission.wdl" as submission
 
-workflow sc2_pubRepo_prep_se {
+workflow mercury_se_prep {
 	input {
 		String 		samplename
 		String		submission_id
@@ -18,7 +18,7 @@ workflow sc2_pubRepo_prep_se {
 
 		String    	gisaid_submitter
     String    	iso_state
-	  String    	iso_country 
+	  String    	iso_country
     String    	iso_continent
     String    	seq_platform
     String    	assembly_method