Merge pull request #192 from CDCgov/fix_null_path_kao

Fix null path error for submission
CDCgov · Apr 4, 2024 · 7495025 · 7495025
2 parents 660bdb7 + 577df14
commit 7495025
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Showing 3 changed files with 15 additions and 3 deletions.
diff --git a/modules/local/initial_submission/main_genbank.nf b/modules/local/initial_submission/main_genbank.nf
@@ -14,7 +14,7 @@ process SUBMISSION_GENBANK {
         'cdcgov/seqsender-dev' : 'cdcgov/seqsender-dev' }"
 
     input:
-    tuple val(meta), path(validated_meta_path), path(fasta_path), path(fastq_1), path(fastq_2), path(annotations_path)
+    tuple val(meta), path(validated_meta_path), path(fasta_path), path(annotations_path)
     path submission_config
 
     // define the command line arguments based on the value of params.submission_test_or_prod, params.send_submission_email

diff --git a/modules/local/initial_submission/main_sra.nf b/modules/local/initial_submission/main_sra.nf
@@ -14,7 +14,7 @@ process SUBMISSION_SRA {
         'cdcgov/seqsender-dev' : 'cdcgov/seqsender-dev'  }"
 
     input:
-    tuple val(meta), path(validated_meta_path), path(fasta_path), path(fastq_1), path(fastq_2)
+    tuple val(meta), path(validated_meta_path), path(fastq_1), path(fastq_2)
     path submission_config
 
     // define the command line arguments based on the value of params.submission_test_or_prod

diff --git a/subworkflows/local/submission.nf b/subworkflows/local/submission.nf
@@ -23,6 +23,7 @@ workflow INITIAL_SUBMISSION {
         // submit the files to database of choice (after fixing config and getting wait time)
         if ( params.genbank && params.sra ){ // genbank and sra
             // submit the files to database of choice (after fixing config and getting wait time)
+            submission_ch.view()
             SUBMISSION_FULL ( submission_ch, submission_config )
 
             // actual process to initiate wait 
@@ -33,7 +34,14 @@ workflow INITIAL_SUBMISSION {
         }
 
         if ( !params.genbank && params.sra ){ //only sra
+            // drop fasta_path from ch
+            submission_ch = submission_ch
+                .map { 
+                    it -> [it[0], it[1], it[3], it[4]] 
+                }
+            submission_ch.view()
             SUBMISSION_SRA ( submission_ch, submission_config )
+
             // actual process to initiate wait 
             WAIT ( SUBMISSION_SRA.out.submission_files.collect(), wait_time )
 
@@ -42,7 +50,11 @@ workflow INITIAL_SUBMISSION {
         }
 
         if ( params.genbank && !params.sra ){ //only genbank
-        // submit the files to database of choice (after fixing config and getting wait time)
+            // drop fastq paths
+            submission_ch = submission_ch
+                .map { 
+                    meta, _, fq1, fq2 -> [meta, fq1, fq2] 
+                }
             SUBMISSION_GENBANK ( submission_ch, submission_config )
 
             // actual process to initiate wait