first commit

tasks/arcashla.wdl

@@ -1,11 +1,12 @@
-task samtools {
+task arcashla {
+    File bam
     String base = basename(bam, ".sorted.bam")
     String docker
     String cluster
 
     command <<<
        mkdir hla_type
-       ./arcasHLA extract ${sorted_bam} -o ${base}.extracted.fq.gz --paired -t 8 -v
+       ./arcasHLA extract ${bam} -o ${base}.extracted.fq.gz --paired -t 8 -v
        ./arcasHLA genotype ${bam}.extracted.1.fq.gz ${bam}.extracted.2.fq.gz hla_type/${base}.genotype.json
     >>>
 

workflow.wdl

@@ -1,6 +1,6 @@
 import "./tasks/hisat2.wdl" as hisat2
 import "./tasks/samtools.wdl" as samtools
-import "./tasks/stringtie.wdl" as stringtie
+import "./tasks/arcashla.wdl" as arcashla
 
 workflow {{ project_name }} {
 
@@ -19,8 +19,8 @@ workflow {{ project_name }} {
                input: sam = hisat2.sam
 	}
 
-        call stringtie.stringtie as stringtie {
-              input: gtf = gtf, bam = samtools.out_bam
+        call arcashla.arcashla as arcashla {
+               input: bam = samtools.out_bam
 	}