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更新 'tasks/featureCounts.wdl'

master
chenqingwang vor 4 Jahren
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Commit
1b9dab80de
1 geänderte Dateien mit 28 neuen und 29 gelöschten Zeilen
  1. +28
    -29
      tasks/featureCounts.wdl

+ 28
- 29
tasks/featureCounts.wdl Datei anzeigen

@@ -1,29 +1,28 @@
task featureCounts {
File bam_file
File lnc_gtf_file = "lncRNAKB_hg38_v7.gtf"
String gtf_dir = "oss://pgx-reference-data/reference/subread/"
String sample_id
String docker
String cluster
Int cpu_num = 4
Int strand_information = 0
command <<<
mkdir -p $sample_id
featureCounts -T $cpu_num -t exon -g gene_id -a $gtf_dir/$lnc_gtf_file -s $strand_information -p -o $sample_id/$sample_id.genefeaturecount.txt $bam_file
>>>
runtime {
docker: docker
cluster: cluster
systemDisk: "cloud_ssd 40"
dataDisk: "cloud_ssd 200 /cromwell_root/"
}
output {
File out_profile = "${sample_id}.genefeaturecount.txt"
File out_summary = "${sample_id}.summary"
}
}
task featureCounts {
File bam_file
File lnc_gtf_file = "lncRNAKB_hg38_v7.gtf"
String gtf_dir = "oss://pgx-reference-data/reference/subread/"
String sample_id
String docker
String cluster
Int cpu_num = 4
Int strand_information = 0

command <<<
featureCounts -T $cpu_num -t exon -g gene_id -a $gtf_dir/$lnc_gtf_file -s $strand_information -p -o $sample_id.genefeaturecount.txt $bam_file
>>>

runtime {
docker: docker
cluster: cluster
systemDisk: "cloud_ssd 40"
dataDisk: "cloud_ssd 200 /cromwell_root/"
}

output {
File out_profile = "${sample_id}.genefeaturecount.txt"
File out_summary = "${sample_id}.summary"
}
}


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