Merge pull request #24 from icgc-argo/decrypt-aspera@0.1.1

[release]
icgc-argo · Aug 18, 2022 · 8813665 · 8813665
2 parents 397f910 + d03c2d3
commit 8813665
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Showing 3 changed files with 11 additions and 14 deletions.
diff --git a/decrypt-aspera/main.nf b/decrypt-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.decrypt-aspera'
@@ -59,7 +60,7 @@ process decryptAspera {
   input:  // input, make update as needed
     path file
     path c4gh_secret_key
-    val c4gh_pass_phrase
+
   output:  // output, make update as needed
     path "*.md5", emit: md5_file
     path "*.{bam,cram,fastq.gz,fq.gz}", emit: output_files
@@ -69,7 +70,7 @@ process decryptAspera {
 
     """
     export C4GH_SECRET_KEY=${c4gh_secret_key}
-    export C4GH_PASSPHRASE=${c4gh_pass_phrase} 
+    export C4GH_PASSPHRASE=${params.c4gh_pass_phrase} 
     python3.6 /tools/main.py \\
       -f ${file} \\
       > decrypt.log 2>&1
@@ -82,7 +83,6 @@ process decryptAspera {
 workflow {
   decryptAspera(
     file(params.file),
-    file(params.c4gh_secret_key),
-    params.c4gh_pass_phrase
+    file(params.c4gh_secret_key)
   )
 }
diff --git a/decrypt-aspera/pkg.json b/decrypt-aspera/pkg.json
@@ -1,6 +1,6 @@
 {
     "name": "decrypt-aspera",
-    "version": "0.1.0",
+    "version": "0.1.1",
     "description": "Decrypt C4GH files",
     "main": "main.nf",
     "deprecated": false,

diff --git a/decrypt-aspera/tests/checker.nf b/decrypt-aspera/tests/checker.nf
@@ -34,7 +34,7 @@
 /* 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.decrypt-aspera'
@@ -53,6 +53,8 @@ params.publish_dir = ""  // set to empty string will disable publishDir
 
 // tool specific parmas go here, add / change as needed
 params.input_file = ""
+params.c4gh_secret_key = ""
+params.c4gh_pass_phrase = ""
 params.expected_output = "./expected/mystery_contents.bam"
 
 include { decryptAspera } from '../main'
@@ -82,15 +84,12 @@ process file_smart_diff {
 workflow checker {
   take:
     input_file
-    c4gh_secret_key
     expected_output
-    c4gh_pass_phrase
 
   main:
     decryptAspera(
-    file(input_file),
-    file(params.c4gh_secret_key),
-    c4gh_pass_phrase
+      file(input_file),
+      file(params.c4gh_secret_key)
    )
 
     file_smart_diff(
@@ -103,8 +102,6 @@ workflow checker {
 workflow {
   checker(
     params.file,
-    params.c4gh_secret_key,
     params.expected_output,
-    params.c4gh_pass_phrase
   )
 }