fixed seqsender typo

CDCgov · Mar 12, 2024 · 323466a · 323466a
1 parent 14fa58c
commit 323466a
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Showing 3 changed files with 9 additions and 5 deletions.
diff --git a/bin/submission_process.py b/bin/submission_process.py
@@ -294,7 +294,7 @@ def update_submission_status(submission_dir, submission_name, organism, test, se
 	if test == True:
 		submission_type = "Test"
 	else:
-		submission_type = "production"
+		submission_type = "Production"
 	# Check if given organism exist in the log
 	df_partial = df.loc[(df["Organism"] == organism) & (df["Submission_Name"] == submission_name) & (df["Submission_Type"] == submission_type)]
 	if df_partial.shape[0] == 0:

diff --git a/modules/local/liftoff_annotation/main.nf b/modules/local/liftoff_annotation/main.nf
@@ -11,7 +11,7 @@ process LIFTOFF {
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'staphb/tostadas:latest' : 'staphb/tostadas:latest' }"
 
-    publishDir "$params.output_dir", mode: 'copy', overwrite: params.overwrite_output
+    //publishDir "$params.output_dir", mode: 'copy', overwrite: params.overwrite_output
 
     input:
     val signal

diff --git a/workflows/tostadas.nf b/workflows/tostadas.nf
@@ -200,18 +200,22 @@ workflow TOSTADAS {
             UPDATE_SUBMISSION (
                 RUN_UTILITY.out,
                 params.submission_config, 
-                INITIAL_SUBMISSION.out.submission_files
+                INITIAL_SUBMISSION.out.submission_files,
+                INITIAL_SUBMISSION.out.submission_log,
+                ''
             )
         }
         // combine the different upload_log csv files together 
         if ( ! params.update_submission ) {
             MERGE_UPLOAD_LOG ( 
-                INITIAL_SUBMISSION.out.submission_files.collect(), INITIAL_SUBMISSION.out.submission_log.collect(), 
+                INITIAL_SUBMISSION.out.submission_files.collect(), 
+                INITIAL_SUBMISSION.out.submission_log.collect(), 
                 '' )
         }
         else {
             MERGE_UPLOAD_LOG ( 
-                UPDATE_SUBMISSION.out.submission_files.collect(), UPDATE_SUBMISSION.out.submission_log.collect(), 
+                UPDATE_SUBMISSION.out.submission_files.collect(), 
+                UPDATE_SUBMISSION.out.submission_log.collect(), 
                 ''
             )
         }