Merge pull request #22 from icgc-argo/download-aspera@0.1.1

[release]
icgc-argo · Aug 18, 2022 · cd41044 · cd41044
2 parents f40f6ba + a481c70
commit cd41044
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Showing 3 changed files with 14 additions and 23 deletions.
diff --git a/download-aspera/main.nf b/download-aspera/main.nf
@@ -18,13 +18,14 @@
 
   Authors:
     Edmund Su
+    Linda Xiang
 */
 
 /********************************************************************/
 /* 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 = '0.1.0'  // package version
+version = '0.1.1'
 
 container = [
     'ghcr.io': 'ghcr.io/icgc-argo/argo-data-submission.download-aspera'
@@ -60,9 +61,8 @@ process downloadAspera {
   input:  // input, make update as needed
     val target_file
     val EGAF
-    val ASCP_SCP_HOST
-    val ASCP_SCP_USER
-    val ASPERA_SCP_PASS
+    val dependency
+
   output:  // output, make update as needed
     path "${EGAF}/${regexed_file_name}", emit: output_file
 
@@ -71,9 +71,9 @@ process downloadAspera {
     regexed_file_name=target_file.replaceAll(/^.*\//,'')
     """
     mkdir ${EGAF}
-    export ASCP_SCP_HOST=${ASCP_SCP_HOST}
-    export ASCP_SCP_USER=${ASCP_SCP_USER}
-    export ASPERA_SCP_PASS=${ASPERA_SCP_PASS}
+    export ASCP_SCP_HOST=${params.ASCP_SCP_HOST}
+    export ASCP_SCP_USER=${params.ASCP_SCP_USER}
+    export ASPERA_SCP_PASS=${params.ASPERA_SCP_PASS}
     python3.6 /tools/main.py \\
       -f ${target_file} \\
       -o ${EGAF} \\
@@ -87,8 +87,6 @@ workflow {
   downloadAspera(
     params.target_file,
     params.EGAF,
-    params.ASCP_SCP_HOST,
-    params.ASCP_SCP_USER,
-    params.ASPERA_SCP_PASS,
+    true
   )
 }
diff --git a/download-aspera/pkg.json b/download-aspera/pkg.json
@@ -1,6 +1,6 @@
 {
     "name": "download-aspera",
-    "version": "0.1.0",
+    "version": "0.1.1",
     "description": "Wrapper to utilize Aspera for EGA downloads",
     "main": "main.nf",
     "deprecated": false,
@@ -34,4 +34,4 @@
     "license": "GNU Affero General Public License v3",
     "bugReport": "https://github.com/icgc-argo/argo-data-submission/issues",
     "homepage": "https://github.com/icgc-argo/argo-data-submission#readme"
-}
+}
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 = '0.1.0'  // package version
+version = '0.1.1'
 
 container = [
     'ghcr.io': 'ghcr.io/icgc-argo/argo-data-submission.download-aspera'
@@ -76,17 +76,13 @@ workflow checker {
   take:
     target_file
     EGAF
-    ASCP_SCP_HOST
-    ASCP_SCP_USER
-    ASPERA_SCP_PASS
+
 
   main:
   downloadAspera(
     params.target_file,
     params.EGAF,
-    params.ASCP_SCP_HOST,
-    params.ASCP_SCP_USER,
-    params.ASPERA_SCP_PASS,
+    true
   )
 
     file_smart_diff(
@@ -98,9 +94,6 @@ workflow checker {
 workflow {
   checker(
     params.target_file,
-    params.EGAF,
-    params.ASCP_SCP_HOST,
-    params.ASCP_SCP_USER,
-    params.ASPERA_SCP_PASS,
+    params.EGAF
   )
 }