added optional schema url to main.nf and removed duplicate sequencing_center

Author: edsu7

payload-gen-seq-experiment/main.nf

@@ -49,7 +49,7 @@ params.experiment_info_tsv = "NO_FILE1"
 params.read_group_info_tsv = "NO_FILE2"
 params.file_info_tsv = "NO_FILE3"
 params.extra_info_tsv = "NO_FILE4"
-
+params.schema_url="NO_FILE5"
 
 process payloadGenSeqExperiment {
   container "${params.container ?: container[params.container_registry ?: default_container_registry]}:${params.container_version ?: version}"
@@ -63,6 +63,7 @@ process payloadGenSeqExperiment {
     path read_group_info_tsv
     path file_info_tsv
     path extra_info_tsv
+    val schema_url
 
   output:
     path "*.sequencing_experiment.payload.json", emit: payload
@@ -72,13 +73,14 @@ process payloadGenSeqExperiment {
     args_read_group_info_tsv = !read_group_info_tsv.name.startsWith("NO_FILE") ? "-r ${read_group_info_tsv}" : ""
     args_file_info_tsv = !file_info_tsv.name.startsWith("NO_FILE") ? "-f ${file_info_tsv}" : ""
     args_extra_info_tsv = !extra_info_tsv.name.startsWith("NO_FILE") ? "-e ${extra_info_tsv}" : ""
-
+    args_schema_url = !schema_url.startsWith("NO_FILE")  ? "-s ${schema_url}" : ""
     """
     main.py \
          ${args_experiment_info_tsv} \
          ${args_read_group_info_tsv} \
          ${args_file_info_tsv} \
-         ${args_extra_info_tsv}
+         ${args_extra_info_tsv} \
+         ${args_schema_url}
     """
 }
 
@@ -90,6 +92,7 @@ workflow {
     file(params.experiment_info_tsv),
     file(params.read_group_info_tsv),
     file(params.file_info_tsv),
-    file(params.extra_info_tsv)
+    file(params.extra_info_tsv),
+    params.schema_url
   )
 }

payload-gen-seq-experiment/main.py

@@ -46,7 +46,7 @@
 TSV_FIELDS['experiment']["conditional"]=[
     "library_isolation_protocol","library_preparation_kit",
     "library_strandedness","rin","dv200","spike_ins_included",
-    "spike_ins_fasta","spike_ins_concentration","sequencing_center",
+    "spike_ins_fasta","spike_ins_concentration",
     "target_capture_kit"]
 
 TSV_FIELDS['read_group']= {}

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

@@ -47,6 +47,7 @@ params.experiment_info_tsv = "NO_FILE1"
 params.read_group_info_tsv = "NO_FILE2"
 params.file_info_tsv = "NO_FILE3"
 params.extra_info_tsv = "NO_FILE4"
+params.schema_url = "NO_FILE5"
 params.expected_output = ""
 
 include { payloadGenSeqExperiment } from '../main'
@@ -82,13 +83,15 @@ workflow checker {
     file_info_tsv
     extra_info_tsv
     expected_output
+    schema_url
 
   main:
     payloadGenSeqExperiment(
       experiment_info_tsv,
       read_group_info_tsv,
       file_info_tsv,
-      extra_info_tsv
+      extra_info_tsv,
+      schema_url
     )
 
     file_smart_diff(
@@ -104,6 +107,7 @@ workflow {
     file(params.read_group_info_tsv),
     file(params.file_info_tsv),
     file(params.extra_info_tsv),
-    file(params.expected_output)
+    file(params.expected_output),
+    params.schema_url
   )
 }