test workflow

tasks/ngscheckmate_fastq.wdl → tasks/fastq_ncm.wdl

@@ -1,4 +1,4 @@
-task ngscheckmate_fastq {
+task fastq_ncm {
   
   File fq1
   File fq2
@@ -13,7 +13,7 @@ task ngscheckmate_fastq {
     set -e
     nt=$(nproc)
     export NCM_HOME=/opt/NGSCheckMate
-    python /opt/NGSCheckMate/ncm_fastq.py -1 ${fq1} -2 ${fq2} /opt/NGSCheckMate/SNP/SNP.pt -p $nt -s ${subsampling_rate} > ${output_id}.vaf
+    python /opt/NGSCheckMate/ngscheckmate_fastq -1 ${fq1} -2 ${fq2} /opt/NGSCheckMate/SNP/SNP.pt -p $nt -s ${subsampling_rate} > ${output_id}.vaf
   >>>
 
   runtime {

tasks/vaf_ncm.wdl

@@ -1,34 +1,32 @@
-task ngscheckmate_fastq {
-  String sample_id
-	File fastq_dir
-	File input_file
-	String docker
-	String cluster_config
-	String disk_size
+task vaf_ncm {
+  
+  Array[File] vaf
+  String docker
+  String cluster_config
+  String disk_size
 
-	command <<<
-		set -o pipefail
-		set -e
-		nt=$(nproc)
-		export NCM_HOME=/opt/NGSCheckMate
-		python /opt/NGSCheckMate/ncm_fastq.py -l ${input_file} -pt /opt/NGSCheckMate/SNP/SNP.pt -O '.' -p $nt -f -s 0.3
-    # rename
-    mv output_all.txt ${sample_id}_output_all.txt
-    mv output_corr_matrix.txt ${sample_id}_output_corr_matrix.txt
-    mv output_matched.txt ${sample_id}_output_matched.txt
-    mv r_script.r ${sample_id}_r_script.r
-	>>>
+  command <<<
+    set -o pipefail
+    set -e
+    nt=$(nproc)
+    export NCM_HOME=/opt/NGSCheckMate
 
-	runtime {
-		docker:docker
-    	cluster:cluster_config
-    	systemDisk:"cloud_ssd 40"
-    	dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
-	}
-	output {
-		File all_txt="${sample_id}_output_all.txt"
-		File cor_txt="${sample_id}_output_corr_matrix.txt"
-		File matched_txt="${sample_id}_output_matched.txt"
-		File r_script="${sample_id}_r_script.r"
-	}
+    mkdir -p /ncm/fastq_vaf
+    cp vaf /ncm/fastq_vaf
+
+    python /opt/NGSCheckMate/vaf_ncm.py -f -I /ncm/fastq_vaf/ -O . -nz $nt
+  >>>
+
+  runtime {
+    docker:docker
+      cluster:cluster_config
+      systemDisk:"cloud_ssd 40"
+      dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
+  }
+  output {
+    File all_txt="output_all.txt"
+    File cor_txt="output_corr_matrix.txt"
+    File r_script="r_script.r"
+    File Rout_script="r_script.r.Rout"
+  }
 }

workflow.wdl

@@ -1,4 +1,5 @@
-import "./tasks/ngscheckmate_fastq.wdl" as ngscheckmate_fastq
+import "./tasks/fastq_ncm.wdl" as fastq_ncm
+import "./tasks/vaf_ncm.wdl" as vaf_ncm
 
 workflow {{ project_name }} {
   
@@ -11,7 +12,7 @@ workflow {{ project_name }} {
   String disk_size
 
   scatter (idx in range(length(fastq1))) {
-    call ngscheckmate_fastq.ngscheckmate_fastq as ngscheckmate_fastq {
+    call fastq_ncm.fastq_ncm as fastq_ncm {
       input:
       fq1=fastq1[idx],
       fq2=fastq2[idx],
@@ -21,4 +22,12 @@ workflow {{ project_name }} {
       cluster_config=cluster_config
     }
   }
+  
+  call vaf_ncm.vaf_ncm as vaf_ncm {
+    input:
+    vaf=fastq_ncm.vaf,
+    docker=docker,
+    disk_size=disk_size,
+    cluster_config=cluster_config
+  }
 }