Merge pull request #166 from icgc-argo-workflows/payload-gen-seq-experiment@0.8.2

[release]

Author: edsu7

payload-gen-seq-experiment/main.nf

@@ -26,7 +26,7 @@
 /* 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 = '0.8.1'
+version = '0.8.2'
 
 container = [
     'ghcr.io': 'ghcr.io/icgc-argo-workflows/data-processing-utility-tools.payload-gen-seq-experiment'
@@ -85,7 +85,6 @@ process payloadGenSeqExperiment {
     args_metadata_payload_json= !metadata_payload_json.name.startsWith("NO_FILE") ? "-m ${metadata_payload_json}" : ""
     args_schema_url = !schema_url.startsWith("NO_FILE")  ? "-s ${schema_url}" : ""
     args_converted_file_args = !cram_reference.startsWith("NO_FILE")  ? "-br ${cram_reference} -b ${converted_files}" : ""
-    args_recalculate_size_and_md5_files = recalculate_size_and_md5_files.empty() ? "" : "-z ${recalculate_size_and_md5_files}"
     """
     main.py \
          ${args_experiment_info_tsv} \

payload-gen-seq-experiment/main.py

@@ -392,7 +392,7 @@ def main(metadata,url,bam_from_cram,bam_from_cram_reference,recalculate_size_and
                         help="BAM files that have converted from CRAM")
     parser.add_argument("-br", "--bam-from-cram-reference",default=None,
                         help="Name of reference file used in cram2bam conversion")
-    parser.add_argument("-z", "--recalculate-size-and-md5-files",default=[],nargs="+",
+    parser.add_argument("-z", "--recalculate-size-and-md5-files",default=[],nargs="*",
                         help="Supplied files here will have their md5sum and size relcalculated")                        
     args = parser.parse_args()
 

payload-gen-seq-experiment/pkg.json

@@ -1,6 +1,6 @@
 {
     "name": "payload-gen-seq-experiment",
-    "version": "0.8.1",
+    "version": "0.8.2",
     "description": "SONG payload generation for sequencing experiment",
     "main": "main.nf",
     "deprecated": false,

payload-gen-seq-experiment/tests/checker.nf

@@ -31,7 +31,7 @@
 /* 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 = '0.8.1'
+version = '0.8.2'
 
 container = [
     'ghcr.io': 'ghcr.io/icgc-argo-workflows/data-processing-utility-tools.payload-gen-seq-experiment'