prepare junction bed and gtf with novel transcripts for PGA input
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- task stringtie {
- File bam
- File anno_gtf
- String docker
- String sample_id
- String cluster
-
- command <<<
- nt=$(nproc)
- /opt/conda/bin/stringtie -p $nt -G ${anno_gtf} -o ${sample_id}.gtf -l CUFF ${bam}
- >>>
-
- runtime {
- docker: docker
- cluster: cluster
- systemDisk: "cloud_ssd 40"
- dataDisk: "cloud_ssd 150 /cromwell_root/"
- }
-
- output {
- File gtf = "${sample_id}.gtf"
- }
- }
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