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feat(wdl): Add Minimap2 whole genome alignment workflows
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| version 1.0 | ||
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| import "../../tasks/alignment/minimap2.wdl" as minimap2 | ||
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| workflow Minimap2RefIndex { | ||
| meta { | ||
| description: "Create a Minimap2 index of a reference genome" | ||
| } | ||
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| input { | ||
| File ref_fasta | ||
| String preset = "asm5" | ||
| String? extra_params | ||
| String? out_prefix | ||
| } | ||
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| parameter_meta { | ||
| ref_fasta: "Reference genome in FASTA format (can be gzipped)." | ||
| preset: "Minimap2 preset to use." | ||
| extra_params: "Extra parameters to pass to minimap2" | ||
| out_prefix: "Prefix for the output index file name." | ||
| } | ||
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| String prefix = select_first([out_prefix, basename(ref_fasta)]) | ||
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| call minimap2.IndexWithMinimap2 { | ||
| input: | ||
| ref_fasta = ref_fasta, | ||
| preset = preset, | ||
| extra_params = extra_params, | ||
| out_prefix = prefix | ||
| } | ||
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| output { | ||
| File mmi = IndexWithMinimap2.mmi | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,36 @@ | ||
| version 1.0 | ||
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| import "../../tasks/alignment/minimap2.wdl" as minimap2 | ||
| import "../../tasks/alignment/samtools.wdl" as samtools | ||
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| workflow Minimap2WGA { | ||
| meta { | ||
| description: "Align reads to a reference genome using Minimap2, requiring an existing minimap2 index. If provided with multiple query fastas (e.g., multiple haplotypes), will merge resulting BAMs." | ||
| } | ||
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| input { | ||
| File ref_fasta_mmi | ||
| Array[File] query_fasta | ||
| String? extra_params | ||
| String out_prefix = "aligned" | ||
| } | ||
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| scatter (fasta in query_fasta) { | ||
| call minimap2.Minimap2WithIx { | ||
| input: | ||
| ref_mmi = ref_fasta_mmi, | ||
| query_fasta = fasta, | ||
| extra_params = extra_params, | ||
| } | ||
| } | ||
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| call samtools.Merge as Merge { | ||
| input: | ||
| bams = Minimap2WithIx.bam, | ||
| out_prefix = out_prefix | ||
| } | ||
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| output { | ||
| File bam = Merge.bam | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,56 @@ | ||
| version 1.0 | ||
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| import "../../structs/Structs.wdl" | ||
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| task Merge { | ||
| input { | ||
| Array[File] bams | ||
| String out_prefix = "merged" | ||
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| RuntimeAttr? runtime_attr_override | ||
| } | ||
| Int disk_size = 1 + 10*ceil(size(bams, "GB")) | ||
| RuntimeAttr default_attr = object { | ||
| cpu_cores: 2, | ||
| mem_gb: 16, | ||
| disk_gb: disk_size, | ||
| boot_disk_gb: 20, | ||
| preemptible_tries: 3, | ||
| max_retries: 2, | ||
| docker: "us-central1-docker.pkg.dev/broad-dsp-lrma/pangenome-pipelines/minimap2:latest" | ||
| } | ||
| RuntimeAttr runtime_attr = select_first([runtime_attr_override, default_attr]) | ||
| Int num_cpu = select_first([runtime_attr.cpu_cores, default_attr.cpu_cores]) | ||
| meta { | ||
| description: "Merge multiple BAM files into a single BAM file" | ||
| } | ||
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| parameter_meta { | ||
| bams: "List of BAM files to merge" | ||
| out_prefix: "Prefix for the output BAM file name" | ||
| runtime_attr: "Runtime attributes for the task" | ||
| } | ||
| command <<< | ||
| set -euxo pipefail | ||
| samtools merge -@ ~{num_cpu} -o ~{out_prefix}.bam ~{sep=" " bams} | ||
| >>> | ||
| output { | ||
| File bam = "~{out_prefix}.bam" | ||
| } | ||
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| runtime { | ||
| cpu: select_first([runtime_attr.cpu_cores, default_attr.cpu_cores]) | ||
| memory: select_first([runtime_attr.mem_gb, default_attr.mem_gb]) + " GiB" | ||
| disks: "local-disk " + select_first([runtime_attr.disk_gb, default_attr.disk_gb]) + " HDD" | ||
| bootDiskSizeGb: select_first([runtime_attr.boot_disk_gb, default_attr.boot_disk_gb]) | ||
| preemptible: select_first([runtime_attr.preemptible_tries, default_attr.preemptible_tries]) | ||
| maxRetries: select_first([runtime_attr.max_retries, default_attr.max_retries]) | ||
| docker: select_first([runtime_attr.docker, default_attr.docker]) | ||
| } | ||
| } |