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report reference genome length in align_reads output; use this value for assemble_refbased. reference_genome_length #538

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Jun 4, 2024
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report reference genome length in align_reads output; use this value for assemble_refbased. reference_genome_length #538

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1 change: 1 addition & 0 deletions pipes/WDL/tasks/tasks_assembly.wdl
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Expand Up @@ -652,6 +652,7 @@ task align_reads {
File aligned_only_reads_bam_idx = "~{sample_name}.mapped.bai"
File aligned_only_reads_fastqc = "~{sample_name}.mapped_fastqc.html"
File aligned_only_reads_fastqc_zip = "~{sample_name}.mapped_fastqc.zip"
Int reference_length = read_int("assembly_length")
Int reads_provided = read_int("reads_provided")
Int reads_aligned = read_int("reads_aligned")
Int read_pairs_aligned = read_int("read_pairs_aligned")
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2 changes: 1 addition & 1 deletion pipes/WDL/workflows/assemble_refbased.wdl
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Expand Up @@ -194,7 +194,7 @@ workflow assemble_refbased {
File align_to_ref_variants_vcf_gz = call_consensus.sites_vcf_gz
Int assembly_length = call_consensus.assembly_length
Int assembly_length_unambiguous = call_consensus.assembly_length_unambiguous
Int reference_genome_length = plot_ref_coverage.assembly_length
Int reference_genome_length = align_to_ref.reference_length[0]
Float assembly_mean_coverage = plot_ref_coverage.mean_coverage

Int dist_to_ref_snps = call_consensus.dist_to_ref_snps
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