Merge pull request #64 from icgc-argo/[email protected]

[release]
icgc-argo · Jan 30, 2023 · 54882ff · 54882ff
2 parents f2e5939 + 121ab14
commit 54882ff
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Showing 4 changed files with 13 additions and 5 deletions.
diff --git a/download-aspera/main.nf b/download-aspera/main.nf
@@ -25,7 +25,7 @@
 /* this block is auto-generated based on info from pkg.json where   */
 /* changes can be made if needed, do NOT modify this block manually */
 nextflow.enable.dsl = 2
-version = '0.1.2'
+version = '0.1.3'
 
 container = [
     'ghcr.io': 'ghcr.io/icgc-argo/argo-data-submission.download-aspera'
@@ -60,11 +60,12 @@ process downloadAspera {
 
   input:  // input, make update as needed
     val target_file
+    val file
     val ega_file_id
     val dependency
 
   output:  // output, make update as needed
-    path "${ega_file_id}/${regexed_file_name}", emit: output_file
+    path "${ega_file_id}/${file}.c4gh", emit: output_file
 
   script:
     // add and initialize variables here as needed
@@ -78,6 +79,7 @@ process downloadAspera {
       -f ${target_file} \\
       -o ${ega_file_id} \\
       > download.log 2>&1
+      mv ${ega_file_id}/${target_file.replaceAll(/^.*\//,'')} ${ega_file_id}/${file}.c4gh
     """
 }
 
@@ -86,6 +88,7 @@ process downloadAspera {
 workflow {
   downloadAspera(
     params.target_file,
+    params.file,
     params.ega_file_id,
     true
   )

diff --git a/download-aspera/pkg.json b/download-aspera/pkg.json
@@ -1,6 +1,6 @@
 {
     "name": "download-aspera",
-    "version": "0.1.2",
+    "version": "0.1.3",
     "description": "Wrapper to utilize Aspera for EGA downloads",
     "main": "main.nf",
     "deprecated": false,

diff --git a/download-aspera/tests/checker.nf b/download-aspera/tests/checker.nf
@@ -29,7 +29,7 @@
 /* this block is auto-generated based on info from pkg.json where   */
 /* changes can be made if needed, do NOT modify this block manually */
 nextflow.enable.dsl = 2
-version = '0.1.2'
+version = '0.1.3'
 
 container = [
     'ghcr.io': 'ghcr.io/icgc-argo/argo-data-submission.download-aspera'
@@ -44,6 +44,7 @@ params.container = ""
 
 // tool specific parmas go here, add / change as needed
 params.target_file=''
+params.file=''
 params.ega_file_id=''
 params.ascp_scp_host=''
 params.ascp_scp_user=''
@@ -79,12 +80,14 @@ process file_smart_diff {
 workflow checker {
   take:
     target_file
+    file
     ega_file_id
 
 
   main:
     downloadAspera(
       target_file,
+      file,
       ega_file_id,
       true
     )
@@ -98,6 +101,7 @@ workflow checker {
 workflow {
   checker(
     params.target_file,
+    params.file,
     params.ega_file_id
   )
 }
diff --git a/download-aspera/tests/test-job-aspera.json b/download-aspera/tests/test-job-aspera.json
@@ -1,7 +1,8 @@
 {
     "target_file" : "/aspera-test-dir-large/100MB", 
+    "file":"example",
     "ega_file_id" : "EGAF000001",
     "ascp_scp_host" : "demo.asperasoft.com",
     "ascp_scp_user" : "aspera",
     "aspera_scp_pass" : "demoaspera"
-}
+}