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expose read_utils.py::fastq_to_bam in wdl task and workflow #1002

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expose read_utils.py::fastq_to_bam in wdl task and workflow #1002

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8f70582
add fastq_to_bam wdl task and workflow
tomkinsc Feb 5, 2020
2e7cf1e
Merge branch 'master' into ct-add-fastq-to-bam
tomkinsc Mar 20, 2020
85d9706
Merge branch 'master' into ct-add-fastq-to-bam
tomkinsc Mar 20, 2020
85b9faa
uncomment header param
tomkinsc Mar 20, 2020
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5 changes: 5 additions & 0 deletions pipes/WDL/workflows/fastq_to_bam.wdl
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Original file line number Diff line number Diff line change
@@ -0,0 +1,5 @@
import "tasks_read_utils.wdl" as read_utils

workflow paired_fastqs_to_bam {
call read_utils.fastq_to_bam
}
29 changes: 29 additions & 0 deletions pipes/WDL/workflows/tasks/tasks_read_utils.wdl
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Expand Up @@ -37,4 +37,33 @@ task downsample_bams {
}
}

task fastq_to_bam {
File in_fastq1
File in_fastq2
File? header

# also used for outfile name
String? sample_name = basename(basename(basename(basename(basename(basename(in_fastq1, ".1.fastq"),".1.fq"),".fastq"),".fq"),".fq1"),".fastq1")

command {
read_utils.py fastq_to_bam \
${in_fastq1} \
${in_fastq2} \
${sample_name}.bam \
${'--sampleName=' + sample_name} \
${'--header ' + header} \
--JVMmemory "1g"
}

output {
File out_bam = "${sample_name}.bam"
String viralngs_version = "viral-ngs_version_unknown"
}
runtime {
docker: "quay.io/broadinstitute/viral-ngs"
memory: "3 GB"
cpu: 2
dx_instance_type: "mem1_ssd1_v2_x4"
preemptible: 0
}
}