Merge pull request #97 from icgc-argo/argo-data-submission-wf@1.2.0

[release]
icgc-argo · Mar 12, 2024 · 5c5a3d1 · 5c5a3d1
2 parents 30bb5d3 + 312deb6
commit 5c5a3d1
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Showing 7 changed files with 11 additions and 10 deletions.
diff --git a/argo-data-submission-wf/main.nf b/argo-data-submission-wf/main.nf
@@ -22,7 +22,7 @@
 */
 
 nextflow.enable.dsl = 2
-version = '1.1.0'
+version = '1.2.0'
 
 // universal params go here, change default value as needed
 params.container = ""
@@ -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){

diff --git a/argo-data-submission-wf/pkg.json b/argo-data-submission-wf/pkg.json
@@ -1,6 +1,6 @@
 {
     "name": "argo-data-submission-wf",
-    "version": "1.1.0",
+    "version": "1.2.0",
     "description": "ARGO data submission workflow",
     "main": "main.nf",
     "deprecated": false,

diff --git a/argo-data-submission-wf/tests/checker.nf b/argo-data-submission-wf/tests/checker.nf
@@ -26,7 +26,7 @@
 */
 
 nextflow.enable.dsl = 2
-version = '1.1.0'
+version = '1.2.0'
 
 // universal params
 params.publish_dir = ""

diff --git a/nextflow.config b/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'
     }
 }
diff --git a/test_data/tiny-grch38-chr11-530001-537000.fa.gz b/test_data/tiny-grch38-chr11-530001-537000.fa.gz
diff --git a/test_data/tiny-grch38-chr11-530001-537000.fa.gz.fai b/test_data/tiny-grch38-chr11-530001-537000.fa.gz.fai
@@ -0,0 +1 @@
+chr11	537000	40	50	51
diff --git a/test_data/tiny-grch38-chr11-530001-537000.fa.gz.gzi b/test_data/tiny-grch38-chr11-530001-537000.fa.gz.gzi