added workflow fetch_sra_to_bam_bam_only

broadinstitute · Jul 14, 2024 · 4407ba1 · 4407ba1
1 parent 5f409b4
commit 4407ba1
Showing 1 changed file with 25 additions and 0 deletions.
diff --git a/pipes/WDL/workflows/fetch_sra_to_bam.wdl b/pipes/WDL/workflows/fetch_sra_to_bam.wdl
@@ -38,3 +38,28 @@ workflow fetch_sra_to_bam {
         File   sra_metadata              = Fetch_SRA_to_BAM.sra_metadata
     }
 }
+
+workflow fetch_sra_to_bam_bam_only {
+    meta {
+        description: "Retrieve reads from the NCBI Short Read Archive in unaligned BAM format."
+        author: "Broad Viral Genomics"
+        email:  "viral-ngs@broadinstitute.org"
+        allowNestedInputs: true
+    }
+
+    call terra.check_terra_env
+
+    #if(check_terra_env.is_running_on_terra) {
+    call ncbi_tools.Fetch_SRA_to_BAM_BAM_only {
+        input:
+            email_address = select_first([check_terra_env.user_email, ""])
+    }
+    #}
+    #if(!check_terra_env.is_running_on_terra) {
+    #    call ncbi_tools.Fetch_SRA_to_BAM
+    #}
+
+    output {
+        File   reads_ubam                = Fetch_SRA_to_BAM_BAM_only.reads_ubam
+    }
+}