test validation wdl metaAssembly

microbiomedata · May 7, 2021 · 011ee91 · 011ee91
1 parent 466f903
commit 011ee91
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diff --git a/test_assembly.wdl b/test_assembly.wdl
@@ -0,0 +1,71 @@
+import "jgi_assembly.wdl" as jgi
+
+workflow test_assembly {
+  String bbtools_container="microbiomedata/bbtools:38.90"
+  String spades_container="microbiomedata/spades:3.15.0"
+  String validate_container="mbabinski17/comparejson:0.1"
+  String rename_contig_prefix="scaffold"
+  Float  uniquekmer=1000
+  String? memory="60G"
+  String? threads="8"
+  String? outdir="/vol_b/nmdc_workflows/test_nmdc/metaAssembly/test_output"
+  String  url="https://portal.nersc.gov/cfs/m3408/test_data/Ecoli_10x-int.fastq.gz"
+  String  ref_json="https://raw.githubusercontent.com/microbiomedata/metaAssembly/master/test_output/small_test_stats.json"
+
+  call prepare {
+    input: container=bbtools_container,
+	   url=url,
+           ref_json=ref_json
+  }
+  call jgi.jgi_metaASM as asm {
+    input: input_file=[prepare.fastq],
+           bbtools_container=bbtools_container,
+	   spades_container=spades_container,
+           memory=memory,
+           threads=threads,
+	   uniquekmer=uniquekmer,
+	   rename_contig_prefix=rename_contig_prefix,
+	   outdir=outdir
+  }
+  call validate {
+    input: container=validate_container,
+           refjson=prepare.refjson,
+           user_json=asm.final_asmstat
+  }
+}
+task prepare {
+   String container
+   String ref_json
+   String url
+   command{
+       wget -O "input.fastq.gz" ${url}
+       wget -O "ref_json.json" ${ref_json}
+   }
+   output{
+      File fastq = "input.fastq.gz"
+      File refjson = "ref_json.json"
+   }
+   runtime {
+     memory: "1 GiB"
+     cpu:  2
+     maxRetries: 1
+     docker: container
+   }
+}
+task validate {
+   String container
+   File refjson
+   File user_json
+   command {
+       compare_json.py -i ${refjson} -f ${user_json}
+   }
+   output {
+       Array[String] result = read_lines(stdout())
+   }
+   runtime {
+     memory: "1 GiB"
+     cpu:  1
+     maxRetries: 1
+     docker: container
+   }
+}
diff --git a/test_output/test_assembly.wdl b/test_output/test_assembly.wdl
@@ -0,0 +1,71 @@
+import "jgi_assembly.wdl" as jgi
+
+workflow test_assembly {
+  String bbtools_container="microbiomedata/bbtools:38.90"
+  String spades_container="microbiomedata/spades:3.15.0"
+  String validate_container="mbabinski17/comparejson:0.1"
+  String rename_contig_prefix="scaffold"
+  Float  uniquekmer=1000
+  String? memory="60G"
+  String? threads="8"
+  String? outdir="/vol_b/nmdc_workflows/test_nmdc/metaAssembly/test_output"
+  String  url="https://portal.nersc.gov/cfs/m3408/test_data/Ecoli_10x-int.fastq.gz"
+  String  ref_json="https://raw.githubusercontent.com/microbiomedata/metaAssembly/master/test_output/small_test_stats.json"
+
+  call prepare {
+    input: container=bbtools_container,
+	   url=url,
+           ref_json=ref_json
+  }
+  call jgi.jgi_metaASM as asm {
+    input: input_file=[prepare.fastq],
+           bbtools_container=bbtools_container,
+	   spades_container=spades_container,
+           memory=memory,
+           threads=threads,
+	   uniquekmer=uniquekmer,
+	   rename_contig_prefix=rename_contig_prefix,
+	   outdir=outdir
+  }
+  call validate {
+    input: container=validate_container,
+           refjson=prepare.refjson,
+           user_json=asm.final_asmstat
+  }
+}
+task prepare {
+   String container
+   String ref_json
+   String url
+   command{
+       wget -O "input.fastq.gz" ${url}
+       wget -O "ref_json.json" ${ref_json}
+   }
+   output{
+      File fastq = "input.fastq.gz"
+      File refjson = "ref_json.json"
+   }
+   runtime {
+     memory: "1 GiB"
+     cpu:  2
+     maxRetries: 1
+     docker: container
+   }
+}
+task validate {
+   String container
+   File refjson
+   File user_json
+   command {
+       compare_json.py -i ${refjson} -f ${user_json}
+   }
+   output {
+       Array[String] result = read_lines(stdout())
+   }
+   runtime {
+     memory: "1 GiB"
+     cpu:  1
+     maxRetries: 1
+     docker: container
+   }
+}