fix post json tsv handling

Author: edsu7

argo-data-submission-wf/main.nf

@@ -293,9 +293,9 @@ workflow ArgoDataSubmissionWf {
         )
 
       if (params.skip_sanity_check){
-        experiment_info_tsv=file(payloadJsonToTsvs.out.experiment_tsv)
-        read_group_info_tsv=file(og_read_group_info_tsv)
-        file_info_tsv=file(og_file_info_tsv)        
+        experiment_info_tsv=payloadJsonToTsvs.out.experiment_tsv
+        read_group_info_tsv=payloadJsonToTsvs.out.read_group_tsv
+        file_info_tsv=payloadJsonToTsvs.out.file_tsv       
       } else {
         sanityCheck(
           payloadJsonToTsvs.out.experiment_tsv,
@@ -306,8 +306,8 @@ workflow ArgoDataSubmissionWf {
         )
 
         experiment_info_tsv=sanityCheck.out.updated_experiment_info_tsv
-        read_group_info_tsv=file(og_read_group_info_tsv)
-        file_info_tsv=file(og_file_info_tsv)
+        read_group_info_tsv=payloadJsonToTsvs.out.read_group_tsv
+        file_info_tsv=payloadJsonToTsvs.out.file_tsv 
       }
     } else {
       if (params.skip_sanity_check){

nextflow.config

@@ -76,13 +76,13 @@ profiles {
     rdpc_qa {
         params.song_url      = 'https://submission-song.rdpc-qa.cumulus.genomeinformatics.org'
         params.score_url     = 'https://submission-score.rdpc-qa.cumulus.genomeinformatics.org'
-        params.clinical_url  = 'https://clinical.qa.argo.cancercollaboratory.org'
+        params.clinical_url  = 'https://clinical.argo-qa.cumulus.genomeinformatics.org'
         params.schema_url    = 'https://submission-song.rdpc-qa.cumulus.genomeinformatics.org/schemas/sequencing_experiment'
     }
     rdpc_dev {
         params.song_url      = 'https://submission-song.rdpc-dev.cumulus.genomeinformatics.org'
         params.score_url     = 'https://submission-score.rdpc-dev.cumulus.genomeinformatics.org'
-        params.clinical_url  = 'https://clinical.dev.argo.cancercollaboratory.org'
+        params.clinical_url  = 'https://clinical.argo-dev.cumulus.genomeinformatics.org'
         params.schema_url    = 'https://submission-song.rdpc-dev.cumulus.genomeinformatics.org/schemas/sequencing_experiment'
     }
 }