Merge pull request #23 from icgc-argo/download-pyega3@0.1.3

[release]
icgc-argo · Aug 18, 2022 · 397f910 · 397f910
2 parents cd41044 + 3952bb5
commit 397f910
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Showing 3 changed files with 12 additions and 17 deletions.
diff --git a/download-pyega3/main.nf b/download-pyega3/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 = '0.1.2'
+version = '0.1.3'
 
 container = [
     'ghcr.io': 'ghcr.io/icgc-argo/argo-data-submission.download-pyega3'
@@ -58,17 +59,16 @@ process downloadPyega3 {
 
   input:  // input, make update as needed
     val ega_id
-    val pyega3_ega_user
-    val pyega3_ega_pass
+    val dependency
 
   output:  // output, make update as needed
     path "${ega_id}/*.md5", emit: md5_file
-    path "${ega_id}/*.{bam,cram,fastq.gz,fq.gz,fastq.bz2,fq.bz2,txt.gz,txt.bz2,vcf,bcf}", emit : output_files
+    path "${ega_id}/*.{bam,cram,fastq.gz,fq.gz,fastq.bz2,fq.bz2,txt.gz,txt.bz2,vcf,vcf.gz,bcf}", emit : output_files
   script:
 
     """
-    export PYEGA3_EGA_USER=${pyega3_ega_user}
-    export PYEGA3_EGA_PASS=${pyega3_ega_pass}
+    export PYEGA3_EGA_USER=${params.pyega3_ega_user}
+    export PYEGA3_EGA_PASS=${params.pyega3_ega_pass}
     mkdir -p ${ega_id}
     python3.6 /tools/main.py \\
     	-f ${ega_id} \\
@@ -84,8 +84,7 @@ process downloadPyega3 {
 workflow {
   downloadPyega3(
     params.ega_id,
-    params.pyega3_ega_user,
-    params.pyega3_ega_pass
+    true
   )
 }
 
diff --git a/download-pyega3/pkg.json b/download-pyega3/pkg.json
@@ -1,6 +1,6 @@
 {
     "name": "download-pyega3",
-    "version": "0.1.2",
+    "version": "0.1.3",
     "description": "EGA download client",
     "main": "main.nf",
     "deprecated": false,

diff --git a/download-pyega3/tests/checker.nf b/download-pyega3/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-pyega3'
@@ -75,13 +75,11 @@ process file_smart_diff {
 workflow checker {
   take:
     ega_id
-    pyega3_ega_user
-    pyega3_ega_pass
+
   main:
     downloadPyega3(
       ega_id,
-      pyega3_ega_user,
-      pyega3_ega_pass
+      true
     )
 
     file_smart_diff(
@@ -92,8 +90,6 @@ workflow checker {
 
 workflow {
   checker(
-    params.ega_id,
-    params.pyega3_ega_user,
-    params.pyega3_ega_pass
+    params.ega_id
   )
 }