allow to generate the payload for oxog metrics file only

Author: lindaxiang

tools/payload-gen-dna-seq-qc/payload-gen-dna-seq-qc.nf

@@ -23,7 +23,7 @@
  */
 
 nextflow.enable.dsl=2
-version = '0.5.2.0'
+version = '0.5.3.0'
 
 params.seq_experiment_analysis = ""
 params.qc_files = []

tools/payload-gen-dna-seq-qc/payload-gen-dna-seq-qc.py

@@ -50,11 +50,12 @@ def calculate_md5(file_path):
 
 def get_aligned_seq_basename(qc_files):
     # get aligned bam/cram basename from '*.wgs.grch38.(cram|bam).qc_metrics.tgz'
+    # or '*.wgs.grch38.(cram|bam).oxog_metrics.tgz'
     for f in qc_files:
-        m = re.match(r'(.+?\.(cram|bam))\.qc_metrics\.tgz$', f)
+        m = re.match(r'(.+?\.(cram|bam))\.(qc_metrics|oxog_metrics)\.tgz$', f)
         if m: return(m.group(1))
 
-    sys.exit('Error: missing DNA alignment QC metrics file with patten: *.{bam,cram}.qc_metrics.tgz')
+    sys.exit('Error: missing DNA alignment QC metrics or oxog metrics file with patten: *.{bam,cram}.{qc_metrics, oxog_metrics}.tgz')
 
 
 def insert_filename_friendly_rg_id(metadata):

tools/payload-gen-dna-seq-qc/tests/test-4.nf.json

@@ -0,0 +1,9 @@
+{
+  "seq_experiment_analysis": "data/89176bbc-ffca-4d73-984a-4a92ed931a98.sequencing_experiment.4.analysis.json",
+  "qc_files": [
+                "data/SA610149.3.20200214.wgs.grch38.cram.oxog_metrics.tgz"
+              ],
+  "publish_dir": "output",
+  "cpus": 1,
+  "mem": 0.5
+}