Merge pull request #103 from icgc-argo/payload-gen-seq-experiment.0.2.1

tests passed

Author: junjun-zhang

tools/payload-gen-seq-experiment/payload-gen-seq-experiment.nf

@@ -22,17 +22,23 @@
  */
 
 nextflow.enable.dsl=2
-version = '0.2.0.0'
+version = '0.2.1'
 
 params.metadata_json = "NO_FILE1"
 params.experiment_info_tsv = "NO_FILE2"
 params.read_group_info_tsv = "NO_FILE3"
 params.file_info_tsv = "NO_FILE4"
 
 params.container_version = ''
+params.cpus = 1
+params.mem = 1  // GB
+params.publish_dir = ""
 
 process payloadGenSeqExperiment {
   container "quay.io/icgc-argo/payload-gen-seq-experiment:payload-gen-seq-experiment.${params.container_version ?: version}"
+  cpus params.cpus
+  memory "${params.mem} GB"
+  publishDir "${params.publish_dir}/${task.process.replaceAll(':', '_')}", mode: "copy", enabled: "${params.publish_dir ? true : ''}"
 
   input:
     path metadata_json

tools/payload-gen-seq-experiment/tests/test-job-bam.nf.json

@@ -1,3 +1,4 @@
 {
-  "metadata_json": "data/seq-exp.bam.metadata.json"
+  "metadata_json": "data/seq-exp.bam.metadata.json",
+  "publish_dir": "outdir"
 }

tools/payload-gen-seq-experiment/tests/test-job-fq.tsv.nf.json

@@ -1,5 +1,6 @@
 {
   "experiment_info_tsv": "data/experiment-fq.v2.tsv",
   "read_group_info_tsv": "data/read_group-fq.v2.tsv",
-  "file_info_tsv": "data/file-fq.v2.tsv"
+  "file_info_tsv": "data/file-fq.v2.tsv",
+  "publish_dir": "outdir"
 }