Workflow to rescue short reads for use with other downstream applications

Author: kvg

.dockstore.yml

@@ -30,3 +30,6 @@ workflows:
 - name: SubsetAndAlignBam
   subclass: wdl
   primaryDescriptorPath: /wdl/SubsetAndAlignBam.wdl
+- name: HidiveRescue
+  subclass: wdl
+  primaryDescriptorPath: /wdl/HidiveRescue.wdl

Cargo.lock

@@ -0,0 +1,152 @@
+version 1.0
+
+workflow HidiveRescue {
+    input {
+        File long_reads_bam
+        File long_reads_bai
+
+        File short_reads_cram
+        File short_reads_crai
+
+        String? locus
+        File? loci
+
+        String sample_name
+
+        File ref_fa_with_alt
+        File ref_fai_with_alt
+        File ref_cache_tar_gz
+
+        Int padding = 500
+    }
+
+    if (defined(locus)) { call PrepareLocus { input: locus = select_first([locus]) } }
+    File bed = select_first([PrepareLocus.bed, loci])
+
+    call Fetch {
+        input:
+            bam = long_reads_bam,
+            loci = bed,
+            padding = padding,
+            prefix = sample_name
+    }
+
+    call Rescue {
+        input:
+            long_reads_fasta = Fetch.fasta,
+            short_reads_cram = short_reads_cram,
+            short_reads_crai = short_reads_crai,
+            ref_fa_with_alt = ref_fa_with_alt,
+            ref_fai_with_alt = ref_fai_with_alt,
+            ref_cache_tar_gz = ref_cache_tar_gz,
+            prefix = sample_name
+    }
+
+    output {
+        File rescued_fasta_gz = Rescue.fasta_gz
+    }
+}
+
+task PrepareLocus {
+    input {
+        String locus
+    }
+
+    command <<<
+        set -euxo pipefail
+
+        echo "~{locus}" | \
+            sed 's/,//g' | \
+            sed 's/\|/\t/g' | \
+            sed 's/\(.*\):/\1\t/' | \
+            sed 's/\(.*\)-\(.*\)/\1\t\2/' > locus.bed
+    >>>
+
+    output {
+        File bed = "locus.bed"
+    }
+
+    runtime {
+        docker: "us.gcr.io/broad-dsp-lrma/lr-hidive:0.1.101"
+        memory: "1 GB"
+        cpu: 1
+        disks: "local-disk 1 SSD"
+    }
+}
+
+task Fetch {
+    input {
+        String bam
+        String? locus
+        File? loci
+        Int padding
+
+        String prefix = "out"
+
+        Int disk_size_gb = 2
+        Int num_cpus = 4
+    }
+
+    command <<<
+        set -euxo pipefail
+
+        hidive fetch -l ~{select_first([locus, loci])} -p ~{padding} ~{bam} > ~{prefix}.fa
+    >>>
+
+    output {
+        File fasta = "~{prefix}.fa"
+    }
+
+    runtime {
+        docker: "us.gcr.io/broad-dsp-lrma/lr-hidive:0.1.107"
+        memory: "2 GB"
+        cpu: num_cpus
+        disks: "local-disk ~{disk_size_gb} SSD"
+    }
+}
+
+task Rescue {
+    input {
+        File long_reads_fasta
+        File short_reads_cram
+        File short_reads_crai
+
+        File ref_fa_with_alt
+        File ref_fai_with_alt
+        File ref_cache_tar_gz
+
+        String prefix = "out"
+
+        Int num_cpus = 16
+    }
+
+    Int disk_size_gb = 1 + 2*ceil(size([long_reads_fasta, short_reads_cram, short_reads_crai, ref_fa_with_alt, ref_fai_with_alt, ref_cache_tar_gz], "GB"))
+    Int memory_gb = 2*num_cpus
+
+    command <<<
+        set -euxo pipefail
+
+        mv ~{ref_fa_with_alt} Homo_sapiens_assembly38.fasta
+        mv ~{ref_fai_with_alt} Homo_sapiens_assembly38.fasta.fai 
+        mv ~{ref_cache_tar_gz} Homo_sapiens_assembly38.ref_cache.tar.gz
+
+        tar xzf Homo_sapiens_assembly38.ref_cache.tar.gz >/dev/null 2>&1
+
+        export REF_PATH="$(pwd)/ref/cache/%2s/%2s/%s:http://www.ebi.ac.uk/ena/cram/md5/%s"
+        export REF_CACHE="$(pwd)/ref/cache/%2s/%2s/%s"
+
+        hidive rescue -r Homo_sapiens_assembly38.fasta -f ~{long_reads_fasta} ~{short_reads_cram} | gzip > ~{prefix}.fa.gz
+    >>>
+
+    output {
+        File fasta_gz = "~{prefix}.fa.gz"
+    }
+
+    runtime {
+        docker: "us.gcr.io/broad-dsp-lrma/lr-hidive:0.1.101"
+        memory: "~{memory_gb} GB"
+        cpu: num_cpus
+        disks: "local-disk ~{disk_size_gb} SSD"
+        maxRetries: 2
+    }
+}