Merge pull request #61 from stjude/wrap

Updates to stjude_seaseq

dnanexus/stjude_seaseq/Readme.developer.md

@@ -1,4 +1,4 @@
-# stjude_seaseaq Developer Readme
+# seaseq Developer Readme
 
 <!--
 TODO: Please edit this Readme.developer.md file to include information

dnanexus/stjude_seaseq/Readme.md

@@ -1,7 +1,7 @@
 <!-- dx-header -->
-# Run St. Jude SEAseq workflow (DNAnexus Platform App)
+# Run SEAseq workflow (DNAnexus Platform App)
 
-Run the SEAseq workflow
+SEAseq workflow
 
 This is the source code for an app that runs on the DNAnexus Platform.
 For more information about how to run or modify it, see

dnanexus/stjude_seaseq/dxapp.json

@@ -1,7 +1,7 @@
 {
- "name": "stjude_seaseaq",
- "title": "Run the St. Jude SEAseq workflow",
- "summary": "stjude_seaseaq",
+ "name": "seaseq",
+ "title": "Run SEAseq workflow",
+ "summary": "Run SEAseq workflow",
  "dxapi": "1.0.0",
  "version": "0.0.1",
  "inputSpec": [
@@ -472,7 +472,7 @@
  }
  },
  "interpreter": "bash",
- "file": "src/stjude_seaseaq.sh",
+ "file": "src/stjude_seaseq.sh",
  "distribution": "Ubuntu",
  "release": "20.04",
  "version": "0",

dnanexus/stjude_seaseq/src/stjude_seaseq.sh

@@ -16,6 +16,7 @@ main() {
  echo '476621564b3b310b17598ee1f02a1865 dxWDL-v1.50.jar' > dxWDL-v1.50.jar.md5
  md5sum -c dxWDL-v1.50.jar.md5
 
+ sed -ibak "s/cloud=\"false\"/cloud=\"true\"/" seaseq.wdl
  dx mkdir -p "${DX_PROJECT_CONTEXT_ID}":/apps/
  wf_id=$(java -jar dxWDL-v1.50.jar compile seaseq.wdl -project "${DX_PROJECT_CONTEXT_ID}" -folder /apps -force -extras dnanexus/extras.json)
  echo "Workflow ID: ${wf_id}"
@@ -29,4 +30,6 @@ main() {
  | jq ".output" \
  | grep -v "reorg_status" \
  | jq 'walk(if type == "object" then with_entries(select(.key | test("^stage-outputs|dnanexus_link|^___$") )) else . end) | walk( if type == "object" then with_entries( .key |= if startswith("stage-outputs") then sub( "^stage-outputs."; "") else . end ) else . end ) |walk( if type == "object" then with_entries( .key |= if endswith("___dxfiles") then sub( "___dxfiles$"; "") else . end ) else . end ) | walk (if (type == "object" and has("___")) then .|=.___ else . end)' > /home/dnanexus/job_output.json
+
+ dx rm -rf "${DX_PROJECT_CONTEXT_ID}":/apps/
 }

seaseq.wdl

@@ -18,8 +18,8 @@ workflow seaseq {
  String pipeline_ver = 'v1.0.0'
 
  meta {
- title: 'SEASEQ Pipeline'
- summary: 'Single-End Antibody Sequencing (SEASEQ) Pipeline'
+ title: 'SEAseq Analysis'
+ summary: 'Single-End Antibody Sequencing (SEAseq) Pipeline'
  description: 'A comprehensive automated computational pipeline for all ChIP-Seq/CUT&RUN data analysis.'
  version: '1.0.0'
  details: {
@@ -31,7 +31,7 @@ workflow seaseq {
  upstreamUrl: 'https://github.com/stjude/seaseq',
  whatsNew: [
  {
- version: "1.1",
+ version: "1.0",
  changes: ["Initial release"]
  }
  ]