do not save haplotype bams and output trio merged bam

PacificBiosciences · Nov 21, 2023 · a88f0c2 · a88f0c2
1 parent d1b2510
commit a88f0c2
Show file tree

Hide file tree

Showing 2 changed files with 4 additions and 6 deletions.
diff --git a/workflows/de_novo_assembly_trio/de_novo_assembly_trio.wdl b/workflows/de_novo_assembly_trio/de_novo_assembly_trio.wdl
@@ -116,7 +116,9 @@ workflow de_novo_assembly_trio {
 		Array[Array[File]] assembly_lowQ_beds = flatten(assemble_genome.assembly_lowQ_beds)
 		Array[Array[File]] zipped_assembly_fastas = flatten(assemble_genome.zipped_assembly_fastas)
 		Array[Array[File]] assembly_stats = flatten(assemble_genome.assembly_stats)
-		Array[Array[IndexData]] asm_bams = flatten(assemble_genome.asm_bams)
+
+		Array[Array[IndexData]] merged_bams = flatten(assemble_genome.merged_bams)
+
 	}
 
 	parameter_meta {

diff --git a/workflows/main.wdl b/workflows/main.wdl
@@ -66,11 +66,7 @@ workflow de_novo_assembly {
 		Array[Array[File]?] zipped_assembly_fastas = de_novo_assembly_sample.zipped_assembly_fastas
 		Array[Array[File]?] assembly_stats = de_novo_assembly_sample.assembly_stats
 
-		#ORIGINAL - UNSURE OF THIS ONE
-		#Array[Array[IndexData]?] asm_bam = de_novo_assembly_sample.asm_bams
-		Array[Array[IndexData]?] asm_bam = de_novo_assembly_sample.asm_bams
 		Array[Array[IndexData]?] merged_bams = de_novo_assembly_sample.merged_bams
-
 		Array[Array[IndexData]?] paftools_vcf = de_novo_assembly_sample.paftools_vcfs
 		Array[Array[File]?] paftools_vcf_stats = de_novo_assembly_sample.paftools_vcf_stats
 
@@ -80,7 +76,7 @@ workflow de_novo_assembly {
 		Array[Array[File]]? trio_assembly_lowQ_beds = de_novo_assembly_trio.assembly_lowQ_beds
 		Array[Array[File]]? trio_zipped_assembly_fastas = de_novo_assembly_trio.zipped_assembly_fastas
 		Array[Array[File]]? trio_assembly_stats = de_novo_assembly_trio.assembly_stats
-		Array[Array[IndexData]]? trio_asm_bams = de_novo_assembly_trio.asm_bams
+		Array[Array[IndexData]]? trio_merged_asm_bams = de_novo_assembly_trio.merged_bams
 	}
 
 	parameter_meta {