Upgrade to NF20.x + Use secure env (#12)

* update readme * use new take syntax * updated env usage (untested)
icgc-argo-workflows · Mar 24, 2020 · 3b49104 · 3b49104
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diff --git a/README.md b/README.md
@@ -1,7 +1,5 @@
 # nextflow-data-processing-utility-tools
 
-_WORK IN PROGRESS AND NOT READY FOR USE!!!_
-
 This repository intends to provide a data utilities for use in Nextflow workflows. Specifically at this time it provides processes wrapping Overture SONG/SCORE clients for upload and download of files and metadata.
 
 Using Nextflow's experimental DSL2, the modules defined in the repo can be imported and used as part of a larger workflow (or independently).

diff --git a/process/score_download.nf b/process/score_download.nf
@@ -29,6 +29,7 @@ process scoreDownload {
         path analysis
         val study_id
         val analysis_id
+        env ACCESSTOKEN
 
     output:
         path analysis, emit: analysis_json
@@ -38,7 +39,6 @@ process scoreDownload {
     """
     export METADATA_URL=${params.song_url}
     export STORAGE_URL=${params.score_url}
-    export ACCESSTOKEN=${params.api_token}
     export TRANSPORT_PARALLEL=${params.cpus}
     export TRANSPORT_MEMORY=${params.transport_mem}
     

diff --git a/process/score_upload.nf b/process/score_upload.nf
@@ -27,14 +27,14 @@ process scoreUpload {
         val analysis_id
         path manifest
         path upload
+        env ACCESSTOKEN
 
     output:
         val analysis_id, emit: ready_to_publish
 
     """
     export METADATA_URL=${params.song_url}
     export STORAGE_URL=${params.score_url}
-    export ACCESSTOKEN=${params.api_token}
     export TRANSPORT_PARALLEL=${params.cpus}
     export TRANSPORT_MEMORY=${params.transport_mem}
     

diff --git a/process/song_get_analysis.nf b/process/song_get_analysis.nf
@@ -25,14 +25,14 @@ process songGetAnalysis {
     input:
         val study_id
         val analysis_id
+        env CLIENT_ACCESS_TOKEN
 
     output:
         path '*.analysis.json', emit: json
 
 
     """
     export CLIENT_SERVER_URL=${params.song_url}
-    export CLIENT_ACCESS_TOKEN=${params.api_token}
     export CLIENT_STUDY_ID=${study_id}
 
     curl -X GET "${params.song_url}/studies/$study_id/analysis/$analysis_id" -H  "accept: */*" > ${analysis_id}.analysis.json

diff --git a/process/song_manifest.nf b/process/song_manifest.nf
@@ -25,13 +25,13 @@ process songManifest {
         val study_id
         val analysis_id
         path upload
+        env CLIENT_ACCESS_TOKEN
 
     output:
         path 'manifest.txt'
 
     """
     export CLIENT_SERVER_URL=${params.song_url}
-    export CLIENT_ACCESS_TOKEN=${params.api_token}
     export CLIENT_STUDY_ID=${study_id}
 
     sing manifest -a ${analysis_id} -d . -f manifest.txt

diff --git a/process/song_publish.nf b/process/song_publish.nf
@@ -24,13 +24,13 @@ process songPublish {
     input:
         val study_id
         val analysis_id
+        env CLIENT_ACCESS_TOKEN
 
     output:
         val analysis_id, emit: analysis_id
 
     """
     export CLIENT_SERVER_URL=${params.song_url}
-    export CLIENT_ACCESS_TOKEN=${params.api_token}
     export CLIENT_STUDY_ID=${study_id}
 
     sing publish -a  ${analysis_id}

diff --git a/process/song_submit.nf b/process/song_submit.nf
@@ -25,13 +25,13 @@ process songSubmit {
     input:
         val study_id
         path payload
+        env CLIENT_ACCESS_TOKEN
 
     output:
         path 'download_payload.json'
 
     """
     export CLIENT_SERVER_URL=${params.song_url}
-    export CLIENT_ACCESS_TOKEN=${params.api_token}
     export CLIENT_STUDY_ID=${study_id}
 
     sing submit -f ${payload} > download_payload.json

diff --git a/workflow/song_score_download.nf b/workflow/song_score_download.nf
@@ -39,12 +39,12 @@ include songGetAnalysis from '../process/song_get_analysis' params(song_params)
 include scoreDownload from '../process/score_download' params(score_params)
 
 workflow songScoreDownload {
-    get: study_id
-    get: analysis_id
+    take: study_id
+    take: analysis_id
 
     main:
-        songGetAnalysis(study_id, analysis_id)
-        scoreDownload(songGetAnalysis.out.json, study_id, analysis_id)
+        songGetAnalysis(study_id, analysis_id, song_params.api_token)
+        scoreDownload(songGetAnalysis.out.json, study_id, analysis_id, score_params.api_token)
 
     emit:
         analysis_json = songGetAnalysis.out.json

diff --git a/workflow/song_score_upload.nf b/workflow/song_score_upload.nf
@@ -51,25 +51,25 @@ include songPublish from '../process/song_publish' params(song_params)
 include extractAnalysisId from '../process/extract_analysis_id' params(extract_params)
 
 workflow songScoreUpload {
-    get: study_id
-    get: payload
-    get: upload
+    take: study_id
+    take: payload
+    take: upload
 
     main:
         // Create new analysis
-        songSubmit(study_id, payload)
+        songSubmit(study_id, payload, song_params.api_token)
 
         // Extract and save analysis_id
         extractAnalysisId(songSubmit.out)
 
         // Generate file manifest for upload
-        songManifest(study_id, extractAnalysisId.out, upload)
+        songManifest(study_id, extractAnalysisId.out, upload, song_params.api_token)
 
         // Upload to SCORE
-        scoreUpload(extractAnalysisId.out, songManifest.out, upload)
+        scoreUpload(extractAnalysisId.out, songManifest.out, upload, score_params.api_token)
 
         // Publish the analysis
-        songPublish(study_id, scoreUpload.out.ready_to_publish)
+        songPublish(study_id, scoreUpload.out.ready_to_publish, song_params.api_token)
 
     emit:
         analysis_id = songPublish.out.analysis_id